Alignments for a candidate for mcmA in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Sedimenticola selenatireducens DSM 17993

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_029133988.1 A3GO_RS0114395 fused isobutyryl-CoA mutase/GTPase IcmF

Query= BRENDA::Q8Y2U5
         (1099 letters)



>NCBI__GCF_000428045.1:WP_029133988.1
          Length = 1085

 Score = 1556 bits (4028), Expect = 0.0
 Identities = 783/1079 (72%), Positives = 899/1079 (83%), Gaps = 13/1079 (1%)

Query: 23   NKVRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGHNRSVDEVVNAALQEDVQGIAVS 82
            NK+RFVTAASLFDGHDASINIMRRILQ+ G EVIHLGHNRSV E+VNAALQEDVQGIA+S
Sbjct: 18   NKIRFVTAASLFDGHDASINIMRRILQAQGAEVIHLGHNRSVAEIVNAALQEDVQGIAIS 77

Query: 83   SYQGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPAEIRELQDYGVARIYSPEDGQRM 142
            SYQGGHVEY KYM+D L+ RGG+ I+VF GGGGVIVP EI+ L DYGV RI+SPEDGQ+M
Sbjct: 78   SYQGGHVEYLKYMVDMLKERGGQEIRVFAGGGGVIVPEEIKALHDYGVTRIFSPEDGQKM 137

Query: 143  GLAGMIADMVRRCDIDLAAYAPTTLEPVAKGDRRALAQLITALESGRIDPALRQAVHARA 202
            GL GMI   + + D D   +AP +LEPV KGD RAL+Q+IT LE+   D  L + V   A
Sbjct: 138  GLQGMIQFAMEQSDFDPGQFAPDSLEPVIKGDWRALSQIITRLENS--DNTLSEQVSEAA 195

Query: 203  ATA--HTPVLGITGTGGAGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGD 260
             T     PVLGITGTGG+GKSSLTDELIRRFRL Q D+L+IA+I++DP+RRK+GGALLGD
Sbjct: 196  LTVKKQIPVLGITGTGGSGKSSLTDELIRRFRLGQQDQLKIAIIAVDPTRRKTGGALLGD 255

Query: 261  RIRMNAINHPNLFVRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIV 320
            RIRMNAI HPN+F RS+ATR+AS E+ D + D++ AC+   FD IIVET GIGQGDA IV
Sbjct: 256  RIRMNAIEHPNIFFRSVATRDASGEVPDYVADIVKACKLADFDFIIVETPGIGQGDAGIV 315

Query: 321  PHADLSLYVMTPEFGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQW 380
            P  D SLYVMTPEFGA SQLEKIDMLDFAD +AINKFDRKGA+DA+RDV KQVQRN+E +
Sbjct: 316  PLVDASLYVMTPEFGAQSQLEKIDMLDFADFIAINKFDRKGAEDAFRDVRKQVQRNQEAF 375

Query: 381  HAKPEDMPVFGTQASHFNDDGVTALYHALADRLAERGMALAERTLPRPAGTCSTSHDAIV 440
                E+MPV+GT A+ FND+GVTALYH L D+LAE GM ++E +LPR    CST    IV
Sbjct: 376  STPVEEMPVYGTIAARFNDEGVTALYHGLRDKLAELGMTVSEDSLPRGDEKCSTGKQVIV 435

Query: 441  PPARVRYLAEVADTVRGYHRRVDAQSGLARERQQLQASRRMLEAAGAAADVLTALDAQAA 500
            PP R RYLAE+A++VRGY R V  Q+ +ARERQQL  S+RML   G A  ++  LD   A
Sbjct: 436  PPQRARYLAEIAESVRGYKRTVATQARIARERQQLSESKRML---GEAGSMVADLDRLIA 492

Query: 501  ERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTTLRKVVLPPY 560
            ERD  L    +KLL +WP ++++YAGDEYVVKIRD+E+RT +T TTLSGT + KVVLP Y
Sbjct: 493  ERDEALDQRAKKLLEIWPQVKQSYAGDEYVVKIRDKEIRTQITRTTLSGTKIPKVVLPKY 552

Query: 561  EDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALRTNRRFKLVS 620
            ED GE+L+WL+ ENVPG+FPYTAGVFAFKR G    EDPTRMFAGEGDA RTNRRFK +S
Sbjct: 553  EDHGELLKWLLLENVPGTFPYTAGVFAFKREG----EDPTRMFAGEGDAFRTNRRFKKLS 608

Query: 621  EGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDGFDLTSPNTS 680
            E  +AKRLSTAFDSVTLYG DPD RPDIYGK+GN+GVSIATLDD+KVLYDGFDL +P+TS
Sbjct: 609  EHSDAKRLSTAFDSVTLYGCDPDERPDIYGKIGNSGVSIATLDDMKVLYDGFDLCNPSTS 668

Query: 681  VSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQNVRGTVQADI 740
            VSMT+NGPAP ILAMF+N+A+DQ + +F  DNGR+PT+ E  KIRAW L NVRGTVQADI
Sbjct: 669  VSMTVNGPAPMILAMFLNSAIDQQINKFETDNGRQPTDEEIEKIRAWTLSNVRGTVQADI 728

Query: 741  LKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFT 800
            LKEDQGQNTCIFST F+LK+MGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFT
Sbjct: 729  LKEDQGQNTCIFSTEFALKLMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFT 788

Query: 801  LANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANE 860
            LANGFTYVE YLARGM ID+FAPNLSFFFSNGMDPEY+V+GRVARRIWA  MR KYGANE
Sbjct: 789  LANGFTYVETYLARGMDIDEFAPNLSFFFSNGMDPEYTVMGRVARRIWATAMRFKYGANE 848

Query: 861  RSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESV 920
            RSQKLKYH+QTSGRSLHAQE+ FNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPT ESV
Sbjct: 849  RSQKLKYHIQTSGRSLHAQEMDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTEESV 908

Query: 921  RRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERGGVLGAMETG 980
            RRALAIQLIIN EWGL K ENPNQG+FIIDELT+LVE AVL EFER++ERGGVLGAMETG
Sbjct: 909  RRALAIQLIINNEWGLTKNENPNQGAFIIDELTELVEEAVLSEFERISERGGVLGAMETG 968

Query: 981  YQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPAHIELARSSEEEKQRQLARL 1040
            YQRG+IQ+ES+ YE  KHDGSLPI+GVNTF NP+        IELARS+EEEK  Q+ RL
Sbjct: 969  YQRGKIQDESLHYEHMKHDGSLPIIGVNTFLNPKGNEEVT--IELARSTEEEKLSQIKRL 1026

Query: 1041 ADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 1099
             +F+ RHA  A   L+R++ A I+++N+F  LM+AVR CSLGQI++AL+EVGGQYRRNM
Sbjct: 1027 REFNQRHATAADTALERIRSAAINNENIFVELMNAVRSCSLGQISNALYEVGGQYRRNM 1085


Lambda     K      H
   0.320    0.134    0.388 

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: 2803
Number of extensions: 95
Number of successful extensions: 6
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: 1099
Length of database: 1085
Length adjustment: 46
Effective length of query: 1053
Effective length of database: 1039
Effective search space:  1094067
Effective search space used:  1094067
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)

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

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

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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