GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudomonas fluorescens FW300-N2E3

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 AO353_10030 AO353_10030 pyruvate carboxylase subunit A

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10030
          Length = 471

 Score =  412 bits (1060), Expect = e-119
 Identities = 210/462 (45%), Positives = 302/462 (65%), Gaps = 4/462 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           +  K+L+ANRGEIAVR++RAC E+G+R+VA+YS+AD+H  HV+ ADEA++IG A     Y
Sbjct: 1   VIKKILIANRGEIAVRIVRACAEMGIRSVAIYSDADRHALHVKRADEAHSIG-AEPLAGY 59

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+   ++  A +   DA+HPGYGFL+ENAE A    +    ++GPSA+ + R+G+KT+AR
Sbjct: 60  LNPRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFIGPSAEVIRRMGDKTEAR 119

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
             M  A VPV PGT        +     D  GYPV +KA  GGGGRG++  +S DE++  
Sbjct: 120 RSMIKAGVPVTPGTEGNVADIAEALTEGDRIGYPVMLKATSGGGGRGIRRCNSRDELEQA 179

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           F     E    F +A V++EK +  P+HIE QIL D  GNV HL ERDCS+QRR+QK+IE
Sbjct: 180 FPRVISEATKAFGSAEVFLEKCIVNPKHIEAQILGDSFGNVVHLFERDCSIQRRNQKLIE 239

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300
            APSP L+ + R  IG+ + R  +A  Y NAGTVEFL+ +GE YFME+NTR+QVEHT+TE
Sbjct: 240 IAPSPQLTPEQRAYIGDLSVRAAKAVGYENAGTVEFLLAEGEVYFMEMNTRVQVEHTITE 299

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
           E+TG+D+V+ Q+R+A+G  L   Q+D++  G +++FRINAE P+  F P+ G ++ Y  P
Sbjct: 300 EITGIDIVREQIRIASGLPLSVKQEDIQHRGFALQFRINAEDPKNNFLPSFGKITRYYAP 359

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG G+R D A+  G  I   YDSM  KL+V     EE + R  RAL++  ++G++T   +
Sbjct: 360 GGPGVRTDTAIYTGYTIPPFYDSMCLKLVVWALTWEEAMDRGLRALDDMRLQGVKTTAAY 419

Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVA 462
           ++ +L +  FR G   T +++    PE    +++R  PE +A
Sbjct: 420 YQEILRNPEFRSGQFNTSFVES--HPELTNYSIKR-KPEELA 458


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: 639
Number of extensions: 23
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: 471
Length adjustment: 35
Effective length of query: 566
Effective length of database: 436
Effective search space:   246776
Effective search space used:   246776
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:

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