GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_3962 Echvi_3962 Acetyl/propionyl-CoA carboxylase, alpha subunit

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



>FitnessBrowser__Cola:Echvi_3962
          Length = 499

 Score =  432 bits (1110), Expect = e-125
 Identities = 229/499 (45%), Positives = 317/499 (63%), Gaps = 8/499 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           MP   ++LVANRGEIA R+++ I+EMG+ ++AVYSE DK A H  YADE+Y +G AP+  
Sbjct: 1   MPKIRKILVANRGEIALRIMRTIREMGLKSVAVYSEVDKNAPHVLYADESYCLGPAPSHK 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYL  E II+A +    DAIHPGYGFLSEN  FA+ V  AG+ FIGPS E +  + DKL 
Sbjct: 61  SYLLGERIIEACQALGADAIHPGYGFLSENTAFAKKVADAGLIFIGPSPESIEIMGDKLA 120

Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180
            K+  +   +P  PG+D  +  I EA K A +IGYPI++KA++GGGG G+  V ++ +  
Sbjct: 121 AKKAVSHYDIPMVPGTDHAILDIQEAKKTAVEIGYPILIKASAGGGGKGMRIVQDEGEFE 180

Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240
           +  +R    A  AFG   +FIEKY  +PRHIE Q++ D++GNY+  +EREC++QRR+QK+
Sbjct: 181 EQMKRAVSEAQSAFGDGAVFIEKYITSPRHIEIQILADQHGNYLHLFERECSVQRRHQKV 240

Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300
           IEEAPS  +  E R++M +  I   K   Y+  GT E    D + +FYFLE+N RLQVEH
Sbjct: 241 IEEAPSAVVNQEMRKAMGQAAIDVAKACQYYGAGTVE-FIVDEALNFYFLEMNTRLQVEH 299

Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360
           P TE+I   DLV+ QI +A G+ L F+Q+DL   + G AIE R+ AED  NNF    G +
Sbjct: 300 PVTEMITGKDLVREQIFIAEGQALSFAQDDLT--ILGHAIETRVYAEDPTNNFLPDIGKL 357

Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420
             YR P GPG+RVD G   G  +P YYD +++KL+ + E R  AIQ  +RA+ DY I GI
Sbjct: 358 ATYRLPQGPGIRVDDGFREGMEIPIYYDPMIAKLVTFEEDRPKAIQKMVRAIDDYHITGI 417

Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQ---KTDQFVKYLREQEEIKAAIAAEIQSRGLL 477
            TT+   +++M  P FQ G+F T ++ +    +     +  E+EEI A IAA +      
Sbjct: 418 STTLSFARFVMLHPAFQSGEFDTKFVEKHFAPSKLAENFSEEEEEILATIAAYLLPNA-- 475

Query: 478 RTSSTDNKGKAQSKSGWKT 496
           +  ST+  G+ Q+ S WKT
Sbjct: 476 KQPSTNVNGQDQNNSKWKT 494


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: 603
Number of extensions: 34
Number of successful extensions: 3
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: 499
Length adjustment: 34
Effective length of query: 475
Effective length of database: 465
Effective search space:   220875
Effective search space used:   220875
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: 52 (24.6 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:

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