GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Pseudomonas simiae WCS417

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate GFF5513 PS417_28215 pyruvate carboxylase subunit A

Query= metacyc::MONOMER-13597
         (509 letters)



>lcl|FitnessBrowser__WCS417:GFF5513 PS417_28215 pyruvate carboxylase
           subunit A
          Length = 471

 Score =  422 bits (1084), Expect = e-122
 Identities = 222/469 (47%), Positives = 320/469 (68%), Gaps = 10/469 (2%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           ++L+ANRGEIA R+++A  EMG+ ++AVYS+AD++A+H K ADEA+ IG  P L  YLN 
Sbjct: 4   KILIANRGEIAVRIVRACAEMGIRSVAVYSDADRHALHVKRADEAHSIGAEP-LAGYLNP 62

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
             +++ A +   DA+HPGYGFLSENAE A+   + GI FIGPS+EV+R++ DK + +R  
Sbjct: 63  RKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFIGPSAEVIRRMGDKTEARRSM 122

Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185
             AGVP  PG++G V  I EAL   ++IGYP+M+KA SGGGG GI R +++++L   + R
Sbjct: 123 IKAGVPVTPGTEGNVADIHEALTEGDRIGYPVMLKATSGGGGRGIRRCNSREELEQAFPR 182

Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245
               A +AFG A++F+EK  VNP+HIE Q++GD +GN V  +ER+C+IQRRNQKLIE AP
Sbjct: 183 VISEATKAFGSAEVFLEKCIVNPKHIEAQILGDSFGNVVHLFERDCSIQRRNQKLIEIAP 242

Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305
           SP L  E+R  + +  ++  K + Y   GT E  F     + YF+E+N R+QVEH  TE 
Sbjct: 243 SPQLTPEQRAYIGDLSVRAAKAVGYENAGTVE--FLLAEGEVYFMEMNTRVQVEHTITEE 300

Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365
           I  ID+V+ QI++A+G  L   QED+    RG A+++RINAED  NNF  S G +T Y  
Sbjct: 301 ITGIDIVREQIRIASGLPLSVKQEDIQH--RGFALQFRINAEDPKNNFLPSFGKITRYYA 358

Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425
           P GPGVR D+ I +G  +PP+YDS+  KL+V+  + E A+  G+RAL D ++ G+KTT  
Sbjct: 359 PGGPGVRTDTAIYTGYTIPPFYDSMCLKLVVWALTWEEAMDRGLRALDDMRLQGVKTTAA 418

Query: 426 LYKWIMQDPDFQEGKFSTSYIS---QKTDQFVKYLREQEEIKAAIAAEI 471
            Y+ I+++P+F+ G+F+TS++    + T+  +K  R+ EE+  AIAA I
Sbjct: 419 YYQEILRNPEFRSGQFNTSFVESHPELTNYSIK--RKPEELALAIAAAI 465


Lambda     K      H
   0.317    0.135    0.385 

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: 551
Number of extensions: 19
Number of successful extensions: 4
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: 509
Length of database: 471
Length adjustment: 34
Effective length of query: 475
Effective length of database: 437
Effective search space:   207575
Effective search space used:   207575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 preprint 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