GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Azospirillum brasilense Sp245

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 AZOBR_RS12015 AZOBR_RS12015 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__azobra:AZOBR_RS12015
          Length = 447

 Score =  461 bits (1185), Expect = e-134
 Identities = 220/444 (49%), Positives = 312/444 (70%), Gaps = 1/444 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MF KVL+ANRGEIA+R+ RAC E+G++TVAV+S AD    HVR ADE+  IGPA A +SY
Sbjct: 1   MFEKVLIANRGEIALRIHRACREMGIQTVAVHSTADADAMHVRLADESVCIGPASARESY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+  +++ AA    ADAIHPG GFL+ENA+FA  VE+  FT++GP+A+ +  +G+K  A+
Sbjct: 61  LNIPAILSAASITGADAIHPGIGFLSENAQFAEMVEEHGFTFIGPTAEHIRIMGDKVTAK 120

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
             + +  +PVVPG+  P  + E+ + +  + GYP+ IKA  GGGG+G+KV  + D++   
Sbjct: 121 KTVMEQGLPVVPGSDGPVPTLEEAEKIGRETGYPILIKAAAGGGGKGMKVARNPDQLKEA 180

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           ++ A+ E  A F N  VY+EKYL  PRHIE+Q+L DEHGN  H GERDCS+QRRHQKVIE
Sbjct: 181 YQLARGEARAAFGNDEVYIEKYLGKPRHIEIQLLGDEHGNCVHFGERDCSVQRRHQKVIE 240

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300
           EAPSPAL+ + R  IG+ A +   A  Y   GT+EFL EDG+FYF+E+NTR+QVEHT+TE
Sbjct: 241 EAPSPALNAEQRAFIGDLAAKTAAAIGYRGVGTMEFLFEDGQFYFIEMNTRLQVEHTITE 300

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
            +TG+D+V+ Q+RVA G  L + Q D+  +GHS+E R+NAE PE  F P+ G +  Y  P
Sbjct: 301 MITGIDLVREQIRVATGAPLGYGQADIRFQGHSIECRVNAEHPE-TFIPSPGKIDGYHAP 359

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG+G+R+D A+  G  I   YDS+IAKL+V G+ R E L+R  R + E+ I G+ T +P 
Sbjct: 360 GGLGVRVDSALYDGYRIPPHYDSLIAKLVVHGTTRNECLMRLRRTIEEYVIGGVDTTLPL 419

Query: 421 HRLMLTDEAFREGSHTTKYLDEVL 444
           H+ ++  +AF +G++   +L++++
Sbjct: 420 HQRIIAQQAFIDGNYDIHWLEQLM 443


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: 670
Number of extensions: 18
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: 447
Length adjustment: 35
Effective length of query: 566
Effective length of database: 412
Effective search space:   233192
Effective search space used:   233192
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