Alignments for a candidate for pccA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Azospirillum brasilense Sp245

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate AZOBR_RS21105 AZOBR_RS21105 acetyl-CoA carboxylase

Query= reanno::PS:Dsui_0516
         (663 letters)



>FitnessBrowser__azobra:AZOBR_RS21105
          Length = 666

 Score =  828 bits (2139), Expect = 0.0
 Identities = 429/667 (64%), Positives = 517/667 (77%), Gaps = 7/667 (1%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60
           +F KILIANRGEIACRVI+TAR++GIKTVAVYS+AD++AL VEMADEAV IG A S +SY
Sbjct: 1   LFSKILIANRGEIACRVIRTARRLGIKTVAVYSDADRNALHVEMADEAVHIGAAPSAQSY 60

Query: 61  LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120
           L+ D+I+ ACK+TGA+AVHPGYGFLSE  EF   L   GI FIGP  ++I  MGDKIESK
Sbjct: 61  LLIDRIVDACKKTGAQAVHPGYGFLSEKREFQEALAAAGIAFIGPDAHAIQAMGDKIESK 120

Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180
           KLA  A V+T+PGY   I     AV IA+ IGYPVMIKASAGGGGKG+RVA+ND EA EG
Sbjct: 121 KLAKAAGVSTVPGYLGVIADDSEAVTIARDIGYPVMIKASAGGGGKGMRVAWNDEEAREG 180

Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240
           F S  NEAR+SF DDRVF+EKY+ +PRHIEIQVL D  G  +YL ER+CSIQRRHQKVIE
Sbjct: 181 FRSAQNEARSSFADDRVFVEKYIQQPRHIEIQVLADGQGTALYLGERECSIQRRHQKVIE 240

Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300
           EAPSPF+D   RKAMGEQAVALARAV+Y+SAGTVEF+V  A + FYFLEMNTRLQVEHPV
Sbjct: 241 EAPSPFLDAATRKAMGEQAVALARAVDYKSAGTVEFIVD-AERNFYFLEMNTRLQVEHPV 299

Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360
           TEL+TGLDLVE MIRVA GEKL L Q D+ ++GWA+E R+ AEDPFR FLPSTGRL  ++
Sbjct: 300 TELVTGLDLVELMIRVAAGEKLTLKQEDIHLHGWAIESRVYAEDPFRNFLPSTGRLTHYR 359

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PP+E D  VRVDTGVY+GGEISMYYD MIAKL   G++R+ AIARMR+AL+ + IRG+S 
Sbjct: 360 PPSE-DPHVRVDTGVYEGGEISMYYDPMIAKLCSWGSTRDAAIARMREALDQYYIRGVSH 418

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480
           NIPF A+LM + RF  G   T FIA+EYP GF AS +P ++PA+LI VAA +HR   DR 
Sbjct: 419 NIPFLASLMANQRFVEGRLTTNFIAEEYPTGFHASDLPPEEPAVLIAVAAVIHRCLNDRD 478

Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEG-----GYLVTYNGEKYELLSDWRQ 535
            Q+SG++PG++ +V D+WVV+ +G +HPV  +P +G     GY V + G  + + SDW  
Sbjct: 479 IQISGKMPGNKVRVRDDWVVVMDGTQHPVHVRPTDGSPQRIGYTVDFEGRHHVVWSDWTL 538

Query: 536 GQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSK 595
           GQ LF GT NG    +QV+R  + Y+L H G++A + V++  AA L ALMP KA PD+SK
Sbjct: 539 GQPLFRGTVNGAHVCVQVDRVGVGYRLSHSGSQALVKVLTPNAARLDALMPVKAPPDMSK 598

Query: 596 FLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSV 655
           FLLSPMPGLL  V+V  GQEVKAGE LAV+EAMKMENIL+A QD  V K+  T GSSL+V
Sbjct: 599 FLLSPMPGLLVSVAVTEGQEVKAGEVLAVVEAMKMENILRAAQDGTVSKVHATPGSSLAV 658

Query: 656 DEIIIEF 662
           D+ I+EF
Sbjct: 659 DQKILEF 665


Lambda     K      H
   0.319    0.135    0.391 

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: 1170
Number of extensions: 46
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: 663
Length of database: 666
Length adjustment: 38
Effective length of query: 625
Effective length of database: 628
Effective search space:   392500
Effective search space used:   392500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources