Alignments for a candidate for liuB in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Rhodomicrobium vannielii ATCC 17100

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_013418382.1 RVAN_RS03495 biotin carboxylase N-terminal domain-containing protein

Query= reanno::Smeli:SM_b21124
         (662 letters)



>NCBI__GCF_000166055.1:WP_013418382.1
          Length = 684

 Score =  575 bits (1482), Expect = e-168
 Identities = 335/691 (48%), Positives = 429/691 (62%), Gaps = 44/691 (6%)

Query: 2   FSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESYL 61
           F+ LLIANRGEIACRI+RTARR+G+RT+AVYS+AD  A H+  AD+A  IG APA +SYL
Sbjct: 6   FASLLIANRGEIACRIVRTARRMGLRTIAVYSEADARARHMKAADDARLIGPAPARDSYL 65

Query: 62  ASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAKA 121
               I++AA++ GA+A+HPGYGFLSE A F EA AEAG+IFVGPP +AIR+MG K AAKA
Sbjct: 66  DIGRIIEAAKASGAEAVHPGYGFLSEKAAFGEACAEAGLIFVGPPASAIRSMGSKAAAKA 125

Query: 122 LMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPAL 181
           LME +GVPVVPGY G  QDA+  A  A+ +G+PVL+KA AGGGGKGMR V   ++   AL
Sbjct: 126 LMEAAGVPVVPGYGGAAQDAAAFAREAKRLGFPVLLKAVAGGGGKGMRIVRAADELEVAL 185

Query: 182 EAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIEE 241
            AA+REA +AFGD ++++ER++ +PRHIE+Q+F D HGN+V LFER+C+LQRRHQKV+EE
Sbjct: 186 TAAKREAAAAFGDDTLMMERFVERPRHIEVQIFADSHGNVVSLFERECTLQRRHQKVVEE 245

Query: 242 APAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQVE 301
           AP+P +    R A+ DAA +AA AIGYVGAGTVEF+AD TN       +F+EMNTRLQVE
Sbjct: 246 APSPSLDDARREALCDAARKAAAAIGYVGAGTVEFVADETNA------WFIEMNTRLQVE 299

Query: 302 HPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRLT 361
           H VTEAITG+DLVEWQLRVA GE LP +Q +I+  G A EAR+YAED   GFLP+TG +T
Sbjct: 300 HAVTEAITGLDLVEWQLRVAMGETLPLRQEEIARAGHAIEARIYAEDADAGFLPSTGTIT 359

Query: 362 ELSFPEGTS--RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGT 419
           +   P+     R+D+G   GD +TP+YDP++AKLI H   R+AAL RL+  L    I G 
Sbjct: 360 QWRAPQAGQGLRIDTGFGAGDEVTPHYDPMLAKLIAHAPTRAAALARLRGVLSGFEIAGV 419

Query: 420 VTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPG--DEALALAAIFSTGALDPN 477
            TN  FL RL  E    +   DTG I+RE   L A   PG    A A+AAI S  A +  
Sbjct: 420 ATNVAFLARLLGEGAVAANAIDTGYIEREHAGLDASHTPGAVHLAAAVAAILSREADETR 479

Query: 478 RS-TDPWSSLGSWQIWGDAHRMVVIEHADV--RATVTLASRGRDQFAVRAGASTLPVLVL 534
           R   DPWS   +   W       V + A V   A     SRGR  F  R        + L
Sbjct: 480 RDPADPWSPWVAGAAW-------VADAACVAGAAWALFGSRGR-VFEFRGKDGHAFTVRL 531

Query: 535 DRFEGGARLEVAGQKRLIRFSRDR-----------------------EALTLFHGGRNLV 571
           ++   G  L V G+     F R+R                        A+T+F G + + 
Sbjct: 532 EQSRNGMTLAVEGEAARFAFERERGDPHRFAVTLGGARRAIGAVYGDGAVTVFDGPQPIR 591

Query: 572 FHVPDGLTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSAS 631
               D      ++       +APMPG V  +    G ++  G  ++++EAMKME T+ A 
Sbjct: 592 LAPVDPFAAEATTHHHGTGTLAPMPGTVLTLLAEPGASLEAGAPILILEAMKMEHTVRAP 651

Query: 632 REGTIANVHVAEGAQVSEGTVLVTLMEEAAQ 662
             G +A   VA G  VSEG  L+    E A+
Sbjct: 652 SRGRVARYAVAIGDFVSEGAALMEFEAEEAR 682


Lambda     K      H
   0.319    0.135    0.394 

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: 1286
Number of extensions: 56
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: 662
Length of database: 684
Length adjustment: 39
Effective length of query: 623
Effective length of database: 645
Effective search space:   401835
Effective search space used:   401835
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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:

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