GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF1047
          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.

Links

Downloads

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:

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