Alignments for a candidate for glcB in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate WP_078430581.1 BK574_RS25245 malate synthase G

Query= reanno::psRCH2:GFF353
         (726 letters)



>NCBI__GCF_002019605.1:WP_078430581.1
          Length = 727

 Score =  944 bits (2439), Expect = 0.0
 Identities = 464/723 (64%), Positives = 567/723 (78%), Gaps = 2/723 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           M + + VG LQVA  LY FVN EA+PG+G+ +  FW+  +++I + AP+N+ LL +R++L
Sbjct: 1   MKDYLSVGNLQVASALYKFVNTEALPGSGLTSEQFWSSMETLITEFAPENKELLQRREEL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q  I  WH+       +  AYK+FL +IGYL  E EDF+ TT+NVDEEI   AGPQLVVP
Sbjct: 61  QTAISQWHKENKDN-FNFEAYKTFLLDIGYLELEVEDFEITTQNVDEEIVLQAGPQLVVP 119

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           + NAR+ALNAANARWGSLYDALYGTDAI E DGA +G GYN +RG KVI++A++FL++  
Sbjct: 120 VNNARYALNAANARWGSLYDALYGTDAIPEEDGAERGKGYNPVRGEKVISFAKDFLDQVV 179

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL   SH D   Y I   +LVV    G TT L++  +L  +QG       +LLKNNG+HF
Sbjct: 180 PLVNASHKDVEKYTISKDQLVVVHSGGQTTELQDATKLVAYQGHPEDLSTILLKNNGLHF 239

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID    IG++D AGVKD+LMESALTTIMDCEDS+AAVDA+DK  VYRNWLGLMKGDL
Sbjct: 240 EIQIDRDHSIGKSDQAGVKDVLMESALTTIMDCEDSVAAVDAEDKVEVYRNWLGLMKGDL 299

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
                KG + +TR +N +R YT   G+  LTL GRSL+F+RNVGHLMTN+A+LD  G EV
Sbjct: 300 TATFFKGNQTLTRDLNSERSYTSLSGD-TLTLRGRSLMFVRNVGHLMTNNAVLDPNGQEV 358

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+D + TSLIA H+L  N+ R N+  GS+YIVKPKMHG +EVAF+ +LF RVED+LG
Sbjct: 359 PEGILDCMITSLIAKHDLLKNSKRTNSTKGSIYIVKPKMHGSKEVAFSNQLFNRVEDLLG 418

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           L RNTLK+G+MDEERRT++NLK CI E +ERVVFINTGFLDRTGDE+HTSMEAGPM+RK+
Sbjct: 419 LERNTLKIGVMDEERRTSLNLKNCINEVKERVVFINTGFLDRTGDEMHTSMEAGPMIRKS 478

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MK+  W+ +YE +NV+VGLACGLQG+AQIGKGMWA PDLMA ML+QKVG   AGANTAW
Sbjct: 479 DMKSSTWLQSYEQSNVNVGLACGLQGRAQIGKGMWASPDLMAEMLKQKVGQLKAGANTAW 538

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAATLHA+HYH+++V   Q EL K      D IL IP+A ++NWS EE +NELDNN
Sbjct: 539 VPSPTAATLHALHYHQVEVPFVQNELKKGITDLKDSILEIPVAANSNWSAEEVQNELDNN 598

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           +QGILGY+VRWV+QGVGCSKVPDIN++ LMEDRATLRISSQHVANW+ HG+ T++QV+E+
Sbjct: 599 AQGILGYVVRWVDQGVGCSKVPDINNVGLMEDRATLRISSQHVANWIHHGICTEEQVLET 658

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           +KRMA VVD QN+GDP YRPMA DFDNSVAFQAA ELV +G +QP+GYTEP+LHRRR E 
Sbjct: 659 MKRMAAVVDEQNEGDPEYRPMATDFDNSVAFQAACELVFKGIEQPSGYTEPILHRRRIEA 718

Query: 721 KAK 723
           K K
Sbjct: 719 KQK 721


Lambda     K      H
   0.316    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1453
Number of extensions: 49
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 726
Length of database: 727
Length adjustment: 40
Effective length of query: 686
Effective length of database: 687
Effective search space:   471282
Effective search space used:   471282
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate WP_078430581.1 BK574_RS25245 (malate synthase G)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01345.hmm
# target sequence database:        /tmp/gapView.3114967.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1220.8   2.0          0 1220.5   2.0    1.0  1  NCBI__GCF_002019605.1:WP_078430581.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430581.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1220.5   2.0         0         0       2     720 ..       4     721 ..       3     722 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1220.5 bits;  conditional E-value: 0
                             TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknkgvid 74 
                                           + ++g+lqva+ l++fv+ e+lpg g+ +e+fws+++ +++++apen+ell +r+e+q+ai ++h++nk   +
  NCBI__GCF_002019605.1:WP_078430581.1   4 YLSVGNLQVASALYKFVNTEALPGSGLTSEQFWSSMETLITEFAPENKELLQRREELQTAISQWHKENKDNFN 76 
                                           5679********************************************************************* PP

                             TIGR01345  75 keayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvipe 147
                                           +eayk fl +igyl+ e e  +i+t+nvd+ei  qagpqlvvpv+naryalnaanarwgslydalyg+++ipe
  NCBI__GCF_002019605.1:WP_078430581.1  77 FEAYKTFLLDIGYLELEVEDFEITTQNVDEEIVLQAGPQLVVPVNNARYALNAANARWGSLYDALYGTDAIPE 149
                                           ************************************************************************* PP

                             TIGR01345 148 edgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyrg 220
                                           edgae+gk ynp+rgekvi fa++fld+++pl ++s++dv+ky+i  ++l+v    g++t l+d ++ v y+g
  NCBI__GCF_002019605.1:WP_078430581.1 150 EDGAERGKGYNPVRGEKVISFAKDFLDQVVPLVNASHKDVEKYTISKDQLVVVHSGGQTTELQDATKLVAYQG 222
                                           ****************************************************9999***************** PP

                             TIGR01345 221 daadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllglm 293
                                           +  d ++illk+nglh e+qid  h igk+d+a+vkd+++esa+tti+dcedsvaavdaedkv vyrn+lglm
  NCBI__GCF_002019605.1:WP_078430581.1 223 HPEDLSTILLKNNGLHFEIQIDRDHSIGKSDQAGVKDVLMESALTTIMDCEDSVAAVDAEDKVEVYRNWLGLM 295
                                           ************************************************************************* PP

                             TIGR01345 294 kgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvlt 366
                                           kg+l +++ k  ++++r+ln +rsyt+  g++l+l+grsl+fvrnvghlmt+ ++l+ +g+e+pegild+++t
  NCBI__GCF_002019605.1:WP_078430581.1 296 KGDLTATFFKGNQTLTRDLNSERSYTSLSGDTLTLRGRSLMFVRNVGHLMTNNAVLDPNGQEVPEGILDCMIT 368
                                           ************************************************************************* PP

                             TIGR01345 367 svialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlka 439
                                           s+ia++dl++++k  ns kgs+yivkpkmhg++evaf+n+lf+r+edllgler+tlk+gvmdeerrtslnlk 
  NCBI__GCF_002019605.1:WP_078430581.1 369 SLIAKHDLLKNSKRTNSTKGSIYIVKPKMHGSKEVAFSNQLFNRVEDLLGLERNTLKIGVMDEERRTSLNLKN 441
                                           ************************************************************************* PP

                             TIGR01345 440 ciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwa 512
                                           ci++vkerv+fintgfldrtgde+htsmeag+m+rk+dmks++wl++ye++nv+ gl cgl+g+aqigkgmwa
  NCBI__GCF_002019605.1:WP_078430581.1 442 CINEVKERVVFINTGFLDRTGDEMHTSMEAGPMIRKSDMKSSTWLQSYEQSNVNVGLACGLQGRAQIGKGMWA 514
                                           ************************************************************************* PP

                             TIGR01345 513 mpdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentnw 585
                                            pdlmaeml++k++ql+agantawvpsptaatlhalhyh+v+v+ vq+el++   ++ ++ il+ipva n+nw
  NCBI__GCF_002019605.1:WP_078430581.1 515 SPDLMAEMLKQKVGQLKAGANTAWVPSPTAATLHALHYHQVEVPFVQNELKKG-ITDLKDSILEIPVAANSNW 586
                                           **************************************************987.9999*************** PP

                             TIGR01345 586 seeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvlesl 658
                                           s+ee+++eldnn+qgilgyvvrwv+qg+gcskvpdi nv lmedratlrissqh+anw+ hgi + eqvle++
  NCBI__GCF_002019605.1:WP_078430581.1 587 SAEEVQNELDNNAQGILGYVVRWVDQGVGCSKVPDINNVGLMEDRATLRISSQHVANWIHHGICTEEQVLETM 659
                                           ************************************************************************* PP

                             TIGR01345 659 ermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefkek 720
                                           +rma vvd+qn gd+ yrpma ++++svaf+aa +l++kg++qpsgytepilh+rr e k+k
  NCBI__GCF_002019605.1:WP_078430581.1 660 KRMAAVVDEQNEGDPEYRPMATDFDNSVAFQAACELVFKGIEQPSGYTEPILHRRRIEAKQK 721
                                           ************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (727 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 37.02
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources