Aligments for a candidate for pccA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccA in Pseudomonas stutzeri RCH2

Align Propionyl-CoA carboxylase alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate GFF1047 Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= SwissProt::P0DTA4
         (730 letters)



>lcl|FitnessBrowser__psRCH2:GFF1047 Psest_1080 Acetyl/propionyl-CoA
           carboxylase, alpha subunit
          Length = 633

 Score =  493 bits (1269), Expect = e-143
 Identities = 286/669 (42%), Positives = 403/669 (60%), Gaps = 46/669 (6%)

Query: 66  ILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYLNMD 125
           +L+ANRGEIACRV++T K MG+ TVAVHS +DA++ H   AD  + +G A  + SYL +D
Sbjct: 5   LLVANRGEIACRVMRTAKAMGLTTVAVHSAIDATARHAREADIRIDLGGAKPADSYLRID 64

Query: 126 AIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKLLAK 185
            +++A + + AQA+HPGYGFLSEN EFA+ +   G+IF+GP   AI AMG K  +K L +
Sbjct: 65  KLIDAAKASGAQAIHPGYGFLSENAEFARAIEQAGLIFLGPPASAIDAMGSKSAAKALME 124

Query: 186 KAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRFS 245
           +A V  +PG+ G  +D +     A +IGYPV++KA+AGGGGKGM++   + +  +    +
Sbjct: 125 EAGVPLVPGYHGEAQDVETFRAAAEKIGYPVLLKATAGGGGKGMKVVEREADLAEALASA 184

Query: 246 SQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAPS 305
            +EA SSFGD R+L+EK++  PRH+EIQV  D+HGN L+LNER+CSIQRR+QKVVEEAP+
Sbjct: 185 QREAQSSFGDWRMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 244

Query: 306 IFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365
             L  E RRAMGE AV  A+A+ Y  AGTVEFL+D++  F+F+EMNTRLQVEHPVTE IT
Sbjct: 245 PGLTPELRRAMGEAAVKAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 304

Query: 366 GLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPIH 425
           GLDLV   IRVA+G PL   Q  +P+ G A+E R+YAEDP   F LP+ G L  Y+E   
Sbjct: 305 GLDLVAWQIRVARGEPLPISQEQVPLIGHAIEVRLYAEDPDNDF-LPATGTLDLYREAAE 363

Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRGVTHNIALL 485
            PG RVDSG+  G  +S +YDPM+ KLI +G NR EA  R+   LD   + GV  N+A L
Sbjct: 364 GPGRRVDSGVAEGDTVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAVGGVRTNLAFL 423

Query: 486 REVIINSRFVEGDINTKFLSDVYPDGFKGHKLTEDERNQLLAIASSLFVAS-QLRAQRFQ 544
           R V+ +  F E +++T F+                  ++LL  A  L  A  Q  A+ F 
Sbjct: 424 RRVVGHRAFAEAELDTAFI--------------PRHESELLRPAGELSDAFWQQAAECFV 469

Query: 545 EPENSRVPIIKPQVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTSTWNLASPL 604
           + E ++V                 D+ H+  +  SG  F +    +++++    N  S  
Sbjct: 470 QTEPTKV---------------RGDDAHSPWSKRSGLRFGMP---AQISLHLQCNGESRR 511

Query: 605 LSVSIDGTQ---RTIQCLSRDAGGNMSIQFLGTVYKVHILTKLAAELNKFMLEKAAEDTS 661
           L V     Q   RT + + +  G  + +Q+ G    V     +A         +A+    
Sbjct: 512 LKVDPAAPQPNVRTPKAIRQ--GDALYLQWNGEWLAVRAFDPIAE-------AEASHQHH 562

Query: 662 SILHSPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAGKTGKVKSVHCKAGDTVG 721
             L +PM G +V V V+ G  V  G  + V+EAMKM++S+ + + G VKS+ C  G+ V 
Sbjct: 563 GGLTAPMNGSIVRVLVEAGQHVEAGTALIVLEAMKMEHSIRSAQAGVVKSLFCSEGEMVS 622

Query: 722 EGDLLVELE 730
           EG +L+E+E
Sbjct: 623 EGAVLLEME 631


Lambda     K      H
   0.318    0.134    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: 1036
Number of extensions: 41
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 730
Length of database: 633
Length adjustment: 39
Effective length of query: 691
Effective length of database: 594
Effective search space:   410454
Effective search space used:   410454
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 (21.7 bits)
S2: 54 (25.4 bits)

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

Downloads

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

Related tools

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, 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

GapMind for catabolism of small carbon sources