GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Pseudomonas fluorescens FW300-N2C3

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 AO356_12020 AO356_12020 pyruvate carboxylase subunit A

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12020 AO356_12020 pyruvate
           carboxylase subunit A
          Length = 471

 Score =  422 bits (1085), Expect = e-122
 Identities = 222/470 (47%), Positives = 323/470 (68%), Gaps = 10/470 (2%)

Query: 5   SRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLN 64
           +++L+ANRGEIA R+++A  EMG+ ++AVYS+AD++A+H K ADEA+ IG  P L  YLN
Sbjct: 3   TKILIANRGEIAVRIVRACAEMGIRSVAVYSDADRHALHVKRADEAHSIGADP-LAGYLN 61

Query: 65  IEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRL 124
              +++ A +   DA+HPGYGFLSENAE A+   + GI FIGPS+EV+R++ DK + +R 
Sbjct: 62  PRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFIGPSAEVIRRMGDKTEARRS 121

Query: 125 ANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWE 184
              AGVP  PG++G V+ I+EAL   ++IGYP+M+KA SGGGG GI R +++++L   + 
Sbjct: 122 MIKAGVPVTPGTEGNVSGIEEALTEGDRIGYPVMLKATSGGGGRGIRRCNSREELEQAFP 181

Query: 185 RNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEA 244
           R    A +AFG A++F+EK  VNP+HIE Q++GD +GN V  +ER+C+IQRRNQKLIE A
Sbjct: 182 RVISEATKAFGSAEVFLEKCIVNPKHIEAQILGDSFGNVVHLFERDCSIQRRNQKLIEIA 241

Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304
           PSP L  E+R  + +  ++  K + Y   GT E  F     + YF+E+N R+QVEH  TE
Sbjct: 242 PSPQLTPEQRAYIGDLSVRAAKAVGYENAGTVE--FLLAEGEVYFMEMNTRVQVEHTITE 299

Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364
            I  ID+V+ QI++A+G  L   QED+    RG A+++RINAED  NNF  S G +T Y 
Sbjct: 300 EITGIDIVREQIRIASGLPLSVKQEDILH--RGFALQFRINAEDPKNNFLPSFGKITRYY 357

Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424
            P GPGVR D+ I +G  +PP+YDS+  KL+V+  + E A+  G+RAL D ++ G+KTT 
Sbjct: 358 APGGPGVRTDTAIYTGYTIPPFYDSMCLKLVVWALTWEEAMDRGLRALDDMRLQGVKTTA 417

Query: 425 ELYKWIMQDPDFQEGKFSTSYIS---QKTDQFVKYLREQEEIKAAIAAEI 471
             Y+ I+++P+F+ G+F+TS++    + T+  +K  R+ EE+  AIAA I
Sbjct: 418 AYYQEILRNPEFRSGQFNTSFVESHPELTNYSIK--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: 556
Number of extensions: 18
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