GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Pontibacillus litoralis JSM 072002

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_036834456.1 N784_RS09590 methylmalonyl-CoA mutase family protein

Query= BRENDA::Q8Y2U5
         (1099 letters)



>NCBI__GCF_000775615.1:WP_036834456.1
          Length = 1079

 Score = 1289 bits (3335), Expect = 0.0
 Identities = 663/1080 (61%), Positives = 812/1080 (75%), Gaps = 17/1080 (1%)

Query: 25   VRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGHNRSVDEVVNAALQEDVQGIAVSSY 84
            VRFVTA+SLFDGHDASINIMRRILQ+ G EVIHLGHNRSV+EVVNAA+QED QGIA+SSY
Sbjct: 12   VRFVTASSLFDGHDASINIMRRILQASGAEVIHLGHNRSVEEVVNAAIQEDAQGIAMSSY 71

Query: 85   QGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPAEIRELQDYGVARIYSPEDGQRMGL 144
            QGGHVEYFKYMID L+A+G +HI+V+GGGGGVI+P EI+EL DYGVARI+SPEDG+  GL
Sbjct: 72   QGGHVEYFKYMIDLLKAKGADHIRVYGGGGGVIIPREIKELHDYGVARIFSPEDGREYGL 131

Query: 145  AGMIADMVRRCDIDLAAYAPTTLEPVAKGDRRALAQLITALESGRI---DPALRQAVHAR 201
             GMI  M+  CD     +    ++ + +GD +A+A+ IT  E+  I   +PA        
Sbjct: 132  QGMINQMIEACDFQPPLHVEQHMQQLQQGDSQAIARFITYTENTTIHETEPAAAVEKLLE 191

Query: 202  AATAHTPVLGITGTGGAGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGDR 261
              T   PVLGITGTGGAGKSSLTDELIRRF L++    ++A++S+DP++RK+GGALLGDR
Sbjct: 192  QQTKSIPVLGITGTGGAGKSSLTDELIRRF-LNEIPERKVAILSVDPTKRKTGGALLGDR 250

Query: 262  IRMNAINHPNLFVRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIVP 321
            IRMNAI    +++RSLATR++ SE+S ++ + I   +A GFDLI+VETSGIGQGDAA+  
Sbjct: 251  IRMNAIFSDRVYMRSLATRDSRSELSKSIDEAIQVVKAAGFDLIVVETSGIGQGDAAVTD 310

Query: 322  HADLSLYVMTPEFGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQWH 381
              DLS+YVMT EFGA SQLEKIDM+D+AD + INKF++KG+ DA R V KQ +R+   +H
Sbjct: 311  VTDLSMYVMTAEFGAPSQLEKIDMIDYADFIVINKFEQKGSADALRQVRKQYERSHMLFH 370

Query: 382  AKPEDMPVFGTQASHFNDDGVTALYHALADRLAER-GMALAERTLPRPAGTCSTSHDAIV 440
                  P++GT AS FND G   L+ AL D + ++ G    E + P    T     + I+
Sbjct: 371  EDQTTFPIYGTIASQFNDPGTNTLFAALVDLINDKYGW---EESTPFERVTNVEKQNLII 427

Query: 441  PPARVRYLAEVADTVRGYHRRVDAQSGLARERQQLQASRRMLEAAGAAADVLTALDAQAA 500
            PP R +YL ++  TV  YH + + QS  AR+  QL  S  ++E       +LT     AA
Sbjct: 428  PPERQQYLRDIVQTVHHYHEKAEEQSDKARKWYQLTKSANLIEEETMKQQLLTT----AA 483

Query: 501  ERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTTLRKVVLPPY 560
              + +L    ++ L  W DL+  Y+ +     +R++E+   LT  +LSG  + KV LP Y
Sbjct: 484  HYEHQLDPNHKQTLEQWDDLKHRYSQEVMTYAVRNKEITIDLTTESLSGLQIPKVALPTY 543

Query: 561  EDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALRTNRRFKLVS 620
             D G+ L W++REN+PG+FP+TAGVF FKR+G    EDPTR FAGEG   RTNRRF  +S
Sbjct: 544  HDWGDRLLWVLRENIPGAFPFTAGVFPFKRKG----EDPTRQFAGEGTPDRTNRRFHYLS 599

Query: 621  EGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDGFDLTSPNTS 680
            EG  AKRLSTAFDSVTLYGEDPD RPDIYGKVG +GVSI TLDD++ LY GFDL  P TS
Sbjct: 600  EGEAAKRLSTAFDSVTLYGEDPDERPDIYGKVGESGVSICTLDDMQKLYAGFDLCHPTTS 659

Query: 681  VSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQNVRGTVQADI 740
            VSMTINGPAP ILAMF NTA+DQ +  F+   GREP + E  +I+A  +  VRGTVQADI
Sbjct: 660  VSMTINGPAPIILAMFFNTAIDQQIEMFKKQEGREPNQEERDRIKAETISVVRGTVQADI 719

Query: 741  LKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFT 800
            LKEDQGQNTCIFST F+L++MGDIQ+YF+ H V+N+YSVSISGYHIAEAGANPI+QLAFT
Sbjct: 720  LKEDQGQNTCIFSTEFALRMMGDIQQYFIDHDVKNYYSVSISGYHIAEAGANPITQLAFT 779

Query: 801  LANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANE 860
            LANGFTYVE YL+RGM I+ FAPNLSFFFSNG+DPEY+V+GRVARRIWA+ MRDKYGANE
Sbjct: 780  LANGFTYVEYYLSRGMDINKFAPNLSFFFSNGLDPEYTVIGRVARRIWAIVMRDKYGANE 839

Query: 861  RSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESV 920
            RSQKLKYHVQTSGRSLHAQEI FNDIRTTLQAL+AI DNCNSLHTN+YDEAITTPT ESV
Sbjct: 840  RSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALLAIQDNCNSLHTNSYDEAITTPTEESV 899

Query: 921  RRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERGGVLGAMETG 980
            RRA+AIQ+IIN+E+GL K EN  QGSFI++ELT LVE AVL+EFER+ +RGGVLGAME  
Sbjct: 900  RRAMAIQMIINKEFGLTKNENSLQGSFIVEELTHLVEEAVLQEFERMNDRGGVLGAMERQ 959

Query: 981  YQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPA-HIELARSSEEEKQRQLAR 1039
            YQRG+IQEES+ YE +KH G LPI+GVNT+ NP          +ELAR+S+EEK  Q+  
Sbjct: 960  YQRGKIQEESLYYEGKKHSGDLPIIGVNTYLNPNPPSEEDIDSMELARASQEEKMHQIHS 1019

Query: 1040 LADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 1099
            L DF  R+A      LQRL++    + N+FA LM+ V+V SLGQIT+AL+EVGGQYRRNM
Sbjct: 1020 LRDFQERNAQVTENALQRLKQVAKQNGNIFAELMETVKVASLGQITNALYEVGGQYRRNM 1079


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: 2659
Number of extensions: 97
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: 1099
Length of database: 1079
Length adjustment: 46
Effective length of query: 1053
Effective length of database: 1033
Effective search space:  1087749
Effective search space used:  1087749
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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