GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS01925
          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.

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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