GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_12020
          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:

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