GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Rhodobacter ovatus JA234

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 WP_097031309.1 CRO07_RS14095 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_900207575.1:WP_097031309.1
          Length = 448

 Score =  434 bits (1116), Expect = e-126
 Identities = 216/444 (48%), Positives = 291/444 (65%), Gaps = 1/444 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MF K+L+ANRGEIA+RV+RAC E+G+++VAV+S AD    HVR ADE+  IGPA + DSY
Sbjct: 1   MFEKILIANRGEIALRVIRACREMGIKSVAVHSTADADAMHVRMADESVCIGPASSTDSY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L   ++I A     A+A+HPGYGFL+ENA FA+ ++D    ++GP+AD +  +G+K  A+
Sbjct: 61  LSKAAIISACEITGAEAVHPGYGFLSENAAFAQALQDHGIEFIGPTADHIRIMGDKITAK 120

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
             M+   VP VPG+       E    VA   G+PV IKA  GGGGRG+KV  + +E++  
Sbjct: 121 ETMRALGVPCVPGSDGGVPDYEAAIGVAQSIGFPVIIKATAGGGGRGMKVARNAEELEVA 180

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           F TA+ E +A F N  VY+EKYL+ PRHIE+Q+  D  G   HLGERDCSLQRRHQKV E
Sbjct: 181 FRTARSEAKAAFGNDEVYMEKYLQRPRHIEIQVFGDGKGRAVHLGERDCSLQRRHQKVFE 240

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300
           EAP P ++ +LR +IG      V    Y  AGT+EFL EDGEFYF+E+NTR+QVEH VTE
Sbjct: 241 EAPGPVITPELRAKIGRICAEAVARINYIGAGTIEFLYEDGEFYFIEMNTRLQVEHPVTE 300

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
            + G+D+V+ Q+RVAAG  +   Q+ +EI GH++E RINAE     F P  G +  +  P
Sbjct: 301 AIFGVDLVREQIRVAAGLPMSLDQEALEINGHAIEVRINAE-KLPNFTPCPGKVRVFHAP 359

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG+G+RMD A+  G  I   YDS+I KLIV G DR E L R  RAL E  ++G+ T +P 
Sbjct: 360 GGLGVRMDSALYGGYSIPPYYDSLIGKLIVHGRDRPEALARLHRALGELIVDGVDTTVPL 419

Query: 421 HRLMLTDEAFREGSHTTKYLDEVL 444
              +L +   + G +   +L++ L
Sbjct: 420 FHALLAEPDIQHGDYNIHWLEKWL 443


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: 615
Number of extensions: 24
Number of successful extensions: 2
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: 448
Length adjustment: 35
Effective length of query: 566
Effective length of database: 413
Effective search space:   233758
Effective search space used:   233758
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 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