GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Rhodobacter ovatus JA234

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 WP_097029020.1 CRO07_RS00230 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_900207575.1:WP_097029020.1
          Length = 666

 Score =  388 bits (996), Expect = e-112
 Identities = 203/451 (45%), Positives = 291/451 (64%), Gaps = 8/451 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F ++L+ANRGEIA RV+K  ++MG+  +AVYS+AD+ A+H   ADEA +IG  PA  SY+
Sbjct: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSDADRNALHVSMADEAIHIGPPPANQSYI 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
            I+ I++A +++  +A+HPGYGFLSE  +FA A+E AG+ FIGP S  +  + DK+  K+
Sbjct: 62  VIDKIMEAIKQSGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSPAIEAMGDKITSKK 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           LA  AGV T PG  G +   DEA+K++++IGYP+M+KA++GGGG G+    N ++  + +
Sbjct: 122 LAQEAGVSTVPGYMGLIADADEAVKISDQIGYPVMIKASAGGGGKGMRIAWNAEEAREGF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           + +K  A  +FG   +FIEK+   PRHIE Q++ DK+GN V   EREC+IQRRNQK+IEE
Sbjct: 182 QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           APSP L    R++M E      K + Y + GT E    D  ++FYFLE+N RLQVEHP T
Sbjct: 242 APSPFLDEATRKAMGEQACALAKAVGYASAGTVE-FIVDGQKNFYFLEMNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           ELI  IDLV+  I++AAGE LPF Q DL  ++ G A+E R+ AED   NF  S G +T Y
Sbjct: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDL--KINGWAMESRLYAEDPYRNFLPSIGRLTRY 358

Query: 364 REPT-----GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418
           R P         VR D+G+  G  +  YYD +++KL  +  +RE AI+    AL  +++ 
Sbjct: 359 RPPVEAVTPTSVVRNDTGVFEGGEISMYYDPMIAKLCTWAPTREAAIEEMRIALDTFEVE 418

Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQK 449
           GI   +     +M  P F  G  +T++I+++
Sbjct: 419 GIGHNLPFVGAVMDHPRFVSGDITTAFIAEE 449


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: 764
Number of extensions: 39
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: 666
Length adjustment: 36
Effective length of query: 473
Effective length of database: 630
Effective search space:   297990
Effective search space used:   297990
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 24 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