GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Pseudomonas stutzeri RCH2

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate GFF1047 Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= metacyc::MONOMER-13597
         (509 letters)



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

 Score =  364 bits (934), Expect = e-105
 Identities = 198/465 (42%), Positives = 283/465 (60%), Gaps = 4/465 (0%)

Query: 7   VLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNIE 66
           +LVANRGEIA RV++  K MG+T +AV+S  D  A H + AD    +G A   DSYL I+
Sbjct: 5   LLVANRGEIACRVMRTAKAMGLTTVAVHSAIDATARHAREADIRIDLGGAKPADSYLRID 64

Query: 67  HIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLAN 126
            +IDAA+ +   AIHPGYGFLSENAEFA A+E+AG+ F+GP +  +  +  K   K L  
Sbjct: 65  KLIDAAKASGAQAIHPGYGFLSENAEFARAIEQAGLIFLGPPASAIDAMGSKSAAKALME 124

Query: 127 MAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWERN 186
            AGVP  PG  G    ++     AEKIGYP+++KA +GGGG G+  V+ +  L +     
Sbjct: 125 EAGVPLVPGYHGEAQDVETFRAAAEKIGYPVLLKATAGGGGKGMKVVEREADLAEALASA 184

Query: 187 KRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAPS 246
           +R A  +FG   + +EKY + PRH+E Q+  D++GN +   ER+C+IQRR+QK++EEAP+
Sbjct: 185 QREAQSSFGDWRMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 244

Query: 247 PALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTELI 306
           P L  E R +M E  +K  + I Y   GT E    D   +F+F+E+N RLQVEHP TE I
Sbjct: 245 PGLTPELRRAMGEAAVKAAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEHPVTEAI 303

Query: 307 FRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYREP 366
             +DLV  QI++A GE LP SQE +   + G AIE R+ AED  N+F  ++G +  YRE 
Sbjct: 304 TGLDLVAWQIRVARGEPLPISQEQV--PLIGHAIEVRLYAEDPDNDFLPATGTLDLYREA 361

Query: 367 T-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425
             GPG RVDSG+  G  V P+YD ++ KLI +GE+RE A    +  L +  +GG++T + 
Sbjct: 362 AEGPGRRVDSGVAEGDTVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAVGGVRTNLA 421

Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAE 470
             + ++    F E +  T++I +   + ++   E  +     AAE
Sbjct: 422 FLRRVVGHRAFAEAELDTAFIPRHESELLRPAGELSDAFWQQAAE 466


Lambda     K      H
   0.317    0.135    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: 733
Number of extensions: 34
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: 509
Length of database: 633
Length adjustment: 36
Effective length of query: 473
Effective length of database: 597
Effective search space:   282381
Effective search space used:   282381
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 (21.6 bits)
S2: 53 (25.0 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 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