Aligments for a candidate for pccA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccA in Herbaspirillum seropedicae SmR1

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate HSERO_RS01925 HSERO_RS01925 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS01925 HSERO_RS01925 acetyl-CoA
           carboxylase biotin carboxylase subunit
          Length = 459

 Score =  447 bits (1149), Expect = e-130
 Identities = 225/445 (50%), Positives = 304/445 (68%), Gaps = 2/445 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MF K+L+ANRGEIA+R+ RAC ELG++TV V+SEAD+   +V+ ADE+  IGPA +  SY
Sbjct: 1   MFEKILIANRGEIALRIQRACRELGIKTVVVHSEADREAKYVKLADESVCIGPAPSTLSY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+  ++I AA   DA AIHPGYGFL+ENA+FA +VE S F ++GP A+ +  +G+K  A+
Sbjct: 61  LNMPAIISAAEVTDAQAIHPGYGFLSENADFAERVEKSGFVFIGPRAENIRMMGDKVSAK 120

Query: 121 SLMQDADVPVVPGTTEPA-DSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179
             M  A VP VPG+     D+ +++  +A   GYPV IKA GGGGGRG++VVH+E  +  
Sbjct: 121 QAMIRAGVPCVPGSDGALPDNPKEIVQIARKIGYPVIIKAAGGGGGRGMRVVHTEAALIN 180

Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239
                K E  A F N  VY+EKYLE PRH+E+QILADEH     LGERDCS+QRRHQKVI
Sbjct: 181 AVTMTKTEAGAAFGNPEVYMEKYLENPRHVEIQILADEHKQAIWLGERDCSMQRRHQKVI 240

Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299
           EEAP+P +   + E+IGE      R   Y  AGT EFL E+ EFYF+E+NTR+QVEH VT
Sbjct: 241 EEAPAPGIPRKIIEKIGERCAEACRKMNYRGAGTFEFLYENEEFYFIEMNTRVQVEHPVT 300

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           E +TG+D+V+ Q+R+AAGE+L + Q D+E++GH++E RINAE P K F P+ G ++ +  
Sbjct: 301 EMITGVDIVQEQIRIAAGEKLRYRQRDIELKGHAIECRINAEDPFK-FIPSPGRITAWHV 359

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG GIR+D     G  +  +YDSM+ K+I  G+ RE+ + R + AL+E  +EG+ T IP
Sbjct: 360 PGGPGIRVDSHAYSGYFVPPNYDSMVGKVIAYGATREQAIRRMQIALSEMVVEGISTNIP 419

Query: 420 FHRLMLTDEAFREGSHTTKYLDEVL 444
            HR ++ D  F EG     YL+  L
Sbjct: 420 LHRELMVDARFFEGGTNIHYLEHKL 444


Lambda     K      H
   0.312    0.132    0.371 

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: 635
Number of extensions: 21
Number of successful extensions: 3
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: 601
Length of database: 459
Length adjustment: 35
Effective length of query: 566
Effective length of database: 424
Effective search space:   239984
Effective search space used:   239984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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