Alignments for a candidate for glcB in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Rhodobacter viridis JA737

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate WP_110806919.1 C8J30_RS16380 malate synthase G

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



>NCBI__GCF_003217355.1:WP_110806919.1
          Length = 717

 Score =  875 bits (2261), Expect = 0.0
 Identities = 436/723 (60%), Positives = 541/723 (74%), Gaps = 10/723 (1%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTERV+  GLQVA  L  F+  +A+PGTGVD A FWAG  ++IH+  PKNRALL KRD +
Sbjct: 1   MTERVEREGLQVAAELATFIEAQALPGTGVDPARFWAGFSALIHEFGPKNRALLEKRDQM 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+IDAWH    GQ HDA AY++FL EIGYL PE  DF   T   D EIA + GPQLVVP
Sbjct: 61  QARIDAWHLHNRGQGHDATAYRAFLDEIGYLAPEGPDFVIETGPTDAEIASVCGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           I NAR+ALNAANARWGSLYDALYGTDA+     A   PGY+ +RG KVIA+A+ FL+ A 
Sbjct: 121 ITNARYALNAANARWGSLYDALYGTDALGTPPAA---PGYDPVRGAKVIAWAKEFLDTAC 177

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GS   +T    + G L   +  G  TGLK+PAQ  G +G A AP  +LL+NNG+H 
Sbjct: 178 PLVAGSWAQATRLWAQDGGLFADVA-GEETGLKDPAQFAGTRGPAEAPAEILLRNNGLHL 236

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
            ++ DPA PIG +D  G+ D+++ESAL++IMDCEDS+A VDA DK + Y NWLGLM+GDL
Sbjct: 237 ILKRDPAHPIGASDPLGLADLVLESALSSIMDCEDSVATVDATDKVLAYTNWLGLMRGDL 296

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            E + KGG+  TRA+ PD  +T  +G G +TL GR+L+ +RNVG LMT  AIL + G E 
Sbjct: 297 TETVTKGGRSFTRALAPDLTFTAPEG-GSVTLKGRALMLVRNVGPLMTTPAILCRSGAEA 355

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEG+MD + T+L A+H+L       N+ TGS+Y+VKPK+HGPEEVAF    F  VE+VLG
Sbjct: 356 PEGLMDAMITTLCALHDLKRGA---NSTTGSVYVVKPKLHGPEEVAFTCATFAHVEEVLG 412

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LP NT+K+GIMDEERRT+ NLK CI+ A++R+ FIN+GFLDRTGDEI TSMEAGPMV KA
Sbjct: 413 LPANTVKLGIMDEERRTSANLKECIRAAKDRLAFINSGFLDRTGDEIFTSMEAGPMVTKA 472

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MK++ WISAYE+ NVD+GL CGL GKAQIGKGMWA PD MA ML QK+ HPMAGAN AW
Sbjct: 473 EMKSQPWISAYEDRNVDIGLRCGLPGKAQIGKGMWAAPDAMAEMLAQKIAHPMAGANCAW 532

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREK-ASIDDILTIPLAQDTNWSEEEKRNELDN 599
           VPSPTAA LHA HYH++DV+ARQ E+A+ ++   + D+LTIPLA    +SE E   E++N
Sbjct: 533 VPSPTAAVLHATHYHRVDVKARQREIAQLQRPLRLFDLLTIPLAAGRTYSEAEITAEIEN 592

Query: 600 NSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVE 659
           N+QGILGY+VRWV+QG+GCSKVPDI+D+ LMEDRATLRISSQ +ANW+ HG+  + QV++
Sbjct: 593 NAQGILGYVVRWVDQGIGCSKVPDIHDVGLMEDRATLRISSQALANWLHHGICGEPQVMK 652

Query: 660 SLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRRE 719
           + ++MA VVDRQN GDP Y+PM P FD  +AFQAA +LV     Q +GYTEPVLH+RR +
Sbjct: 653 AFRKMAAVVDRQNAGDPAYQPMGPYFD-GLAFQAACDLVFLARIQSSGYTEPVLHQRRAQ 711

Query: 720 FKA 722
            KA
Sbjct: 712 VKA 714


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: 1419
Number of extensions: 67
Number of successful extensions: 7
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: 717
Length adjustment: 40
Effective length of query: 686
Effective length of database: 677
Effective search space:   464422
Effective search space used:   464422
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_110806919.1 C8J30_RS16380 (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.468856.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 1026.6   0.0          0 1026.4   0.0    1.0  1  NCBI__GCF_003217355.1:WP_110806919.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003217355.1:WP_110806919.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1026.4   0.0         0         0       2     719 ..       4     714 ..       3     716 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1026.4 bits;  conditional E-value: 0
                             TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaideyhrknk.gvi 73 
                                           rv+  +lqva++l +f+e ++lpgtgvd + fw+gf+++++++ p+nr ll krd++qa id++h +n+    
  NCBI__GCF_003217355.1:WP_110806919.1   4 RVEREGLQVAAELATFIEAQALPGTGVDPARFWAGFSALIHEFGPKNRALLEKRDQMQARIDAWHLHNRgQGH 76 
                                           678899***************************************************************4568 PP

                             TIGR01345  74 dkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaanarwgslydalygsnvip 146
                                           d +ay+ fl eigyl +e     iet   d+eias  gpqlvvp++naryalnaanarwgslydalyg++++ 
  NCBI__GCF_003217355.1:WP_110806919.1  77 DATAYRAFLDEIGYLAPEGPDFVIETGPTDAEIASVCGPQLVVPITNARYALNAANARWGSLYDALYGTDALG 149
                                           ******************999**************************************************98 PP

                             TIGR01345 147 eedgaekgkeynpkrgekviefarefldeslplesgsyadvvkykivdkklavqlesgkvtrlkdeeqfvgyr 219
                                              +a  g  y+p+rg kvi++a+efld + pl +gs+a++ +    d+ l +++  g++t lkd++qf g r
  NCBI__GCF_003217355.1:WP_110806919.1 150 TPPAA-PG--YDPVRGAKVIAWAKEFLDTACPLVAGSWAQATRLWAQDGGLFADVA-GEETGLKDPAQFAGTR 218
                                           76654.45..*********************************************9.9*************** PP

                             TIGR01345 220 gdaadpevillktnglhielqidarhpigkadkakvkdivlesaittildcedsvaavdaedkvlvyrnllgl 292
                                           g a +p  ill++nglh+ l+ d+ hpig +d+ ++ d+vlesa+++i+dcedsva+vda dkvl y n+lgl
  NCBI__GCF_003217355.1:WP_110806919.1 219 GPAEAPAEILLRNNGLHLILKRDPAHPIGASDPLGLADLVLESALSSIMDCEDSVATVDATDKVLAYTNWLGL 291
                                           ************************************************************************* PP

                             TIGR01345 293 mkgtlkeklekngriikrklnedrsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvl 365
                                           m+g+l e+++k gr ++r l  d ++ta++g  ++l+gr+l++vrnvg lmt+p+il  +g e peg++d+++
  NCBI__GCF_003217355.1:WP_110806919.1 292 MRGDLTETVTKGGRSFTRALAPDLTFTAPEGGSVTLKGRALMLVRNVGPLMTTPAILCRSGAEAPEGLMDAMI 364
                                           ************************************************************************* PP

                             TIGR01345 366 tsvialydlkvqnklrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlk 438
                                           t+++al+dlk+     ns +gsvy+vkpk+hgpeevaf+   f+ +e++lgl+ +t+k+g+mdeerrts nlk
  NCBI__GCF_003217355.1:WP_110806919.1 365 TTLCALHDLKRG---ANSTTGSVYVVKPKLHGPEEVAFTCATFAHVEEVLGLPANTVKLGIMDEERRTSANLK 434
                                           **********95...5********************************************************* PP

                             TIGR01345 439 aciakvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmw 511
                                            ci  +k+r+afin+gfldrtgdei tsmeag+mv ka+mks pw++aye  nv+ gl cgl+gkaqigkgmw
  NCBI__GCF_003217355.1:WP_110806919.1 435 ECIRAAKDRLAFINSGFLDRTGDEIFTSMEAGPMVTKAEMKSQPWISAYEDRNVDIGLRCGLPGKAQIGKGMW 507
                                           ************************************************************************* PP

                             TIGR01345 512 ampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeiltipvaentn 584
                                           a pd maeml +k+  + agan awvpsptaa lha+hyhrvdv++ q e+a+ +r   l ++ltip+a    
  NCBI__GCF_003217355.1:WP_110806919.1 508 AAPDAMAEMLAQKIAHPMAGANCAWVPSPTAAVLHATHYHRVDVKARQREIAQLQRPLRLFDLLTIPLAAGRT 580
                                           ************************************************************************* PP

                             TIGR01345 585 wseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhlanwlrhgivskeqvles 657
                                           +se ei +e++nn+qgilgyvvrwv+qgigcskvpdih+v lmedratlrissq lanwl hgi    qv+++
  NCBI__GCF_003217355.1:WP_110806919.1 581 YSEAEITAEIENNAQGILGYVVRWVDQGIGCSKVPDIHDVGLMEDRATLRISSQALANWLHHGICGEPQVMKA 653
                                           ************************************************************************* PP

                             TIGR01345 658 lermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsgytepilharrlefke 719
                                           + +ma vvd+qnagd+ay+pm + ++  +af+aa dl++    q sgytep+lh+rr + k+
  NCBI__GCF_003217355.1:WP_110806919.1 654 FRKMAAVVDRQNAGDPAYQPMGPYFD-GLAFQAACDLVFLARIQSSGYTEPVLHQRRAQVKA 714
                                           *********************99886.79*****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (717 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 32.15
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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