GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Dinoroseobacter shibae DFL-12

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 3607987 Dshi_1395 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)

Query= SwissProt::I3R7G3
         (601 letters)



>lcl|FitnessBrowser__Dino:3607987 Dshi_1395 acetyl-CoA carboxylase,
           biotin carboxylase (RefSeq)
          Length = 448

 Score =  452 bits (1162), Expect = e-131
 Identities = 223/449 (49%), Positives = 303/449 (67%), Gaps = 1/449 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MFSK+L+ANRGEIA+RV+RAC ELG+++VAV+S AD    HVR ADEA  IGP  +  SY
Sbjct: 1   MFSKILIANRGEIALRVIRACRELGIQSVAVHSTADTDAMHVRMADEAVCIGPPPSPQSY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L   ++I A     A+AIHPGYGFL+ENA F + V+D   T++GP+A+ +  +G+K  A+
Sbjct: 61  LSIPAIISACEITGAEAIHPGYGFLSENANFVQIVQDHGLTFIGPTAEHIRVMGDKITAK 120

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
             M++  VP VPG+       E  + VA + GYPV +KA  GGGGRG+K+  + +++D  
Sbjct: 121 ETMKNLGVPCVPGSDGGVPDLETARRVAGEIGYPVIVKATAGGGGRGMKLAKTAEDLDEA 180

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           F+TA+ EG+A F N  VY+EKYL  PRHIEVQ+  D  G   HLGERDCSLQRRHQKV E
Sbjct: 181 FQTARSEGKAAFGNPDVYLEKYLSTPRHIEVQVFGDGKGGAVHLGERDCSLQRRHQKVFE 240

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300
           EAPSP +  + R RIG+     V   +Y  AGT+EFL E+GEFYF+E+NTR+QVEH VTE
Sbjct: 241 EAPSPVIDAETRARIGKTCAEAVARIDYAGAGTIEFLYENGEFYFIEMNTRLQVEHPVTE 300

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
            + G+D+VK Q+RVAAG  + F Q+++++ GH++E RINAE     F P  G ++T+  P
Sbjct: 301 AIFGVDLVKEQIRVAAGYPMTFKQENLQVRGHAIEVRINAE-KVPAFTPCPGMVTTFHTP 359

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

Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERI 449
              +L +EA + G +T  +L+E L+  +I
Sbjct: 420 FHALLAEEAIQTGDYTIHWLEEWLETAQI 448


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: 610
Number of extensions: 19
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 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 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