Alignments for a candidate for glcB in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Halomonas desiderata SP1

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate WP_086509169.1 BZY95_RS06550 malate synthase G

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



>NCBI__GCF_002151265.1:WP_086509169.1
          Length = 728

 Score =  966 bits (2497), Expect = 0.0
 Identities = 477/729 (65%), Positives = 577/729 (79%), Gaps = 7/729 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           M+ERV    LQVA  L  F+N++A+PGTG+DA +FWAG D++ HDL PKNR LLA+R+ L
Sbjct: 1   MSERVTRHRLQVAAELDRFINDQALPGTGIDAESFWAGVDAIFHDLTPKNRELLAERERL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QAQ+D WH+   G   D   Y++FL+EIGYL+        +T NVD E+A  AGPQLVVP
Sbjct: 61  QAQLDTWHRENPGPVRDMSVYRAFLEEIGYLVDAPAQVTVSTANVDREVAIQAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           + NAR+ALNAANARWGSLYDALYGTDAISE  GA KG GYN  RG KVIAYAR  L+ AA
Sbjct: 121 VSNARYALNAANARWGSLYDALYGTDAISEEGGAEKGSGYNPKRGEKVIAYARGVLDLAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL TGSH D+  Y +  G+LVVSL+ G  TGLK P +L G+ G+A+ P ++LL N+G+H 
Sbjct: 181 PLATGSHRDAVKYVLRDGRLVVSLEGGRETGLKEPGKLVGYSGDAANPESILLSNHGLHL 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQIDP+ PIG+TD AGVKD+L+E+ALT IMDCEDS+AAVDA+DK  VY NWLGLMKGDL
Sbjct: 241 EIQIDPSHPIGKTDPAGVKDLLVEAALTAIMDCEDSVAAVDAEDKVGVYANWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            E +EKGGK  TR ++ DR YT  +G G LTL GRSL+F+RNVGHLMT  A+LD +GNE+
Sbjct: 301 EEAIEKGGKTFTRRLHADRSYTTPEG-GSLTLPGRSLMFVRNVGHLMTTPAVLDADGNEL 359

Query: 361 PEGIMDGLFTSLIAVHNL-NGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVL 419
           PEGI+DG+ TSL+A+H+L  G    +N+R+GS+YIVKPKMHGP+EVAF+ ELFGRVED+L
Sbjct: 360 PEGILDGIVTSLLALHDLKKGENDPRNSRSGSVYIVKPKMHGPKEVAFSNELFGRVEDLL 419

Query: 420 GLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRK 479
           GL R+TLK+GIMDEERRT++NLKACI EA  RVVFINTGFLDRTGDE+HT+MEAGPM+RK
Sbjct: 420 GLARDTLKMGIMDEERRTSVNLKACIAEAASRVVFINTGFLDRTGDEMHTAMEAGPMIRK 479

Query: 480 AAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTA 539
             MK   WI AYE NNV VGLACGL+G+AQIGKGMWAMPDLMAAMLEQK+GHP AGANTA
Sbjct: 480 GDMKNAAWIGAYERNNVLVGLACGLRGRAQIGKGMWAMPDLMAAMLEQKIGHPKAGANTA 539

Query: 540 WVPSPTAATLHAMHYHKIDVQARQVEL-AKREKA----SIDDILTIPLAQDTNWSEEEKR 594
           WVPSPTAATLHA+HYH+IDV   Q EL A+ E A     +D +LT+P+A+   WS+E  +
Sbjct: 540 WVPSPTAATLHALHYHQIDVAEIQRELEAQGEPALLEELLDKLLTVPVAERVEWSDEAIQ 599

Query: 595 NELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTK 654
            ELDNN QGILGY+VRWVE GVGCSKVPDI+D+ LMEDRATLRISSQH+ANW+ HGVV  
Sbjct: 600 QELDNNCQGILGYVVRWVEHGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLHHGVVDA 659

Query: 655 DQVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLH 714
           ++V ++L+RMA VVD QN GDP Y  M+ DF  S AF+AA +L+ +G  QP+GYTEP+LH
Sbjct: 660 ERVQKTLERMAKVVDEQNAGDPAYTAMSADFAASTAFKAASDLIFKGRVQPSGYTEPLLH 719

Query: 715 RRRREFKAK 723
             R   KA+
Sbjct: 720 HWRAVHKAR 728


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: 1517
Number of extensions: 58
Number of successful extensions: 4
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: 728
Length adjustment: 40
Effective length of query: 686
Effective length of database: 688
Effective search space:   471968
Effective search space used:   471968
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_086509169.1 BZY95_RS06550 (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.664430.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 1237.5   0.0          0 1237.4   0.0    1.0  1  NCBI__GCF_002151265.1:WP_086509169.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002151265.1:WP_086509169.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1237.4   0.0         0         0       2     719 ..       4     727 ..       3     728 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1237.4 bits;  conditional E-value: 0
                             TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvi 73 
                                           rv+  rlqva++l +f+++++lpgtg+dae+fw+g+d+i +dl+p+nrella+r+++qa +d +hr+n+ +v 
  NCBI__GCF_002151265.1:WP_086509169.1   4 RVTRHRLQVAAELDRFINDQALPGTGIDAESFWAGVDAIFHDLTPKNRELLAERERLQAQLDTWHRENPgPVR 76 
                                           78899****************************************************************7789 PP

                             TIGR01345  74 dkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvip 146
                                           d + y+ fl+eigylv+ p +vt+ t nvd e+a qagpqlvvpv naryalnaanarwgslydalyg+++i+
  NCBI__GCF_002151265.1:WP_086509169.1  77 DMSVYRAFLEEIGYLVDAPAQVTVSTANVDREVAIQAGPQLVVPVSNARYALNAANARWGSLYDALYGTDAIS 149
                                           ************************************************************************* PP

                             TIGR01345 147 eedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyr 219
                                           ee+gaekg+ ynpkrgekvi++ar  ld + pl +gs++d+vky + d++l+v le g++t lk++ + vgy 
  NCBI__GCF_002151265.1:WP_086509169.1 150 EEGGAEKGSGYNPKRGEKVIAYARGVLDLAAPLATGSHRDAVKYVLRDGRLVVSLEGGRETGLKEPGKLVGYS 222
                                           ************************************************************************* PP

                             TIGR01345 220 gdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllgl 292
                                           gdaa+pe ill ++glh+e+qid+ hpigk+d+a+vkd+++e+a+t+i+dcedsvaavdaedkv vy n+lgl
  NCBI__GCF_002151265.1:WP_086509169.1 223 GDAANPESILLSNHGLHLEIQIDPSHPIGKTDPAGVKDLLVEAALTAIMDCEDSVAAVDAEDKVGVYANWLGL 295
                                           ************************************************************************* PP

                             TIGR01345 293 mkgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvl 365
                                           mkg+l+e +ek g++++r+l  drsyt+++g  l+l+grsl+fvrnvghlmt+p++l+ +g+e+pegildg++
  NCBI__GCF_002151265.1:WP_086509169.1 296 MKGDLEEAIEKGGKTFTRRLHADRSYTTPEGGSLTLPGRSLMFVRNVGHLMTTPAVLDADGNELPEGILDGIV 368
                                           ************************************************************************* PP

                             TIGR01345 366 tsvialydlkv.qnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnl 437
                                           ts++al+dlk+ +n  rnsr gsvyivkpkmhgp+evaf+n+lf+r+edllgl+r+tlk+g+mdeerrts+nl
  NCBI__GCF_002151265.1:WP_086509169.1 369 TSLLALHDLKKgENDPRNSRSGSVYIVKPKMHGPKEVAFSNELFGRVEDLLGLARDTLKMGIMDEERRTSVNL 441
                                           *********9735779********************************************************* PP

                             TIGR01345 438 kaciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgm 510
                                           kacia+++ rv+fintgfldrtgde+ht+meag+m+rk+dmk a+w+ ayernnv+ gl cglrg+aqigkgm
  NCBI__GCF_002151265.1:WP_086509169.1 442 KACIAEAASRVVFINTGFLDRTGDEMHTAMEAGPMIRKGDMKNAAWIGAYERNNVLVGLACGLRGRAQIGKGM 514
                                           ************************************************************************* PP

                             TIGR01345 511 wampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerrae....lkeiltipv 579
                                           wampdlma mle+k++ ++agantawvpsptaatlhalhyh+ dv ++q el ++++ a     l+++lt+pv
  NCBI__GCF_002151265.1:WP_086509169.1 515 WAMPDLMAAMLEQKIGHPKAGANTAWVPSPTAATLHALHYHQIDVAEIQRELEAQGEPALleelLDKLLTVPV 587
                                           *****************************************************9998877556678899**** PP

                             TIGR01345 580 aentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivske 652
                                           ae  +ws+e i++eldnn+qgilgyvvrwve+g+gcskvpdih+v lmedratlrissqh+anwl hg+v  e
  NCBI__GCF_002151265.1:WP_086509169.1 588 AERVEWSDEAIQQELDNNCQGILGYVVRWVEHGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLHHGVVDAE 660
                                           ************************************************************************* PP

                             TIGR01345 653 qvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefke 719
                                           +v+++lermakvvd+qnagd+ay  m+ +++as afkaa+dli+kg  qpsgytep+lh +r   k+
  NCBI__GCF_002151265.1:WP_086509169.1 661 RVQKTLERMAKVVDEQNAGDPAYTAMSADFAASTAFKAASDLIFKGRVQPSGYTEPLLHHWRAVHKA 727
                                           **************************************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (728 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 42.00
//
[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