Alignments for a candidate for mcm-large in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Algoriphagus machipongonensis PR1

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_008201258.1 ALPR1_RS12840 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000166275.1:WP_008201258.1
          Length = 1125

 Score =  264 bits (674), Expect = 2e-74
 Identities = 213/636 (33%), Positives = 320/636 (50%), Gaps = 92/636 (14%)

Query: 5    DKEVLKKIKEEEKRW-EETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYME 63
            +K+ +++  EE  R+ E+  V K  +K  + K    +    +I +I  P    E W  + 
Sbjct: 497  NKKWIEEWPEEVARYSEDFYVFKVRDKEIKVKTYHNSLSETKIPKIALPKY--EAWGDLL 554

Query: 64   KLGF----PGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTG--LS 117
            K G     PG++P+T GV+     G   T R +AG  + E +NKR+ Y +SQ      LS
Sbjct: 555  KWGLRENVPGKFPYTAGVFPFKREGEDPT-RMFAGEGSPERTNKRFHY-VSQDMPAKRLS 612

Query: 118  VAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTA 174
             AFD  T  G D D+ P   G++G  GV +  L D + L+ G  L     S SMTIN  A
Sbjct: 613  TAFDSVTLYGEDPDYRPDIYGKIGNSGVNVCCLDDAKKLYSGFNLVDPLTSVSMTINGPA 672

Query: 175  ANLLAMYILVA---------EEQGVSQE-------------------------------- 193
            A + A ++  A         +EQG+ +E                                
Sbjct: 673  ATMTAFFMNAAIDQQCEVYIKEQGLEKEVDAKIERIFKGKGIPRPVYNGKIPAGNDGLGL 732

Query: 194  KLRGTVQNDILKEYI-----------ARGTY--------------IFPPQPSMRLTTDII 228
             L G   + +L + +            RGT               IF  + S+RL  D+ 
Sbjct: 733  MLLGVSGDQVLPKEVYEKIKAETVSRVRGTVQADILKEDQAQNTCIFSTEFSLRLMGDVQ 792

Query: 229  MYCAEN-VPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRL 287
             Y  ++ +  +  +SISGYHI EAGAN + ++A TL++G  YV+  + RGMD++KFAP L
Sbjct: 793  DYFIDHGIRNFYSVSISGYHIAEAGANPITQLALTLSNGFTYVEYYVSRGMDINKFAPNL 852

Query: 288  SFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPE 346
            SFFF+  N    E A   R ARR+WA  MK  + A N RS ML++H QT+G +L AQ+ +
Sbjct: 853  SFFFS--NGIDPEYAVIGRVARRIWAKAMKLKYGA-NERSQMLKYHIQTSGRSLHAQEID 909

Query: 347  NNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDP 406
             N +R  +QAL A+     SLHTN+YDEA++ PTE SVR A+  Q II  E G+    +P
Sbjct: 910  FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEASVRRAMAIQLIINKELGLSKNENP 969

Query: 407  LGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKR 466
            L GA+ IE LTD + E      ++I + GG++ A+E  Y + +I E +  Y+     G+ 
Sbjct: 970  LQGAFIIEELTDLVEEAIYLEFDRITERGGVLGAMETMYQRGKIQEESMHYEMLKHTGEY 1029

Query: 467  IIVGVNAFVTDEPIEV----EILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAA 522
             I+GVN F++ E        E+++     +E QI+ LK L ++ D + V   L  L+  A
Sbjct: 1030 PIIGVNTFLSSEGSPTVTPGEVIRATEEEKESQIQTLKNL-NQFDPELVSTHLQNLKKIA 1088

Query: 523  EKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558
              E+ N+   ++EA +H  +L E+T  L E+ G+YR
Sbjct: 1089 -VENGNIFSELMEASKH-CSLGEITHALYEVGGQYR 1122


Lambda     K      H
   0.318    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: 1341
Number of extensions: 82
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 563
Length of database: 1125
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1084
Effective search space:   565848
Effective search space used:   565848
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. 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 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