GapMind for catabolism of small carbon sources

 

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

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate Echvi_4494 Echvi_4494 Hemoglobin-like flavoprotein

Query= CharProtDB::CH_003330
         (396 letters)



>FitnessBrowser__Cola:Echvi_4494
          Length = 402

 Score =  257 bits (657), Expect = 4e-73
 Identities = 147/401 (36%), Positives = 220/401 (54%), Gaps = 14/401 (3%)

Query: 1   MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60
           M    TI  VK+T P+L E G ++T  FY ++F  +P+L+ +FNM+NQ  G Q + L NA
Sbjct: 1   MASKSTIEIVKSTAPVLKEYGEQITKVFYKKLFETHPDLRNLFNMTNQVKGTQPKVLANA 60

Query: 61  IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118
           I  YA+ IE    LL AV  IA KH+S  I PE Y IVGE LL  + E+       +++ 
Sbjct: 61  IIQYATYIETPEVLLQAVNSIAHKHSSLSITPEMYPIVGETLLWAIKEVLGDAATPDIIG 120

Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178
           AW +AYG LA +FI +E  IY E  S+  G+ G ++F++V K   +  ITSF L   DG 
Sbjct: 121 AWAEAYGELAEIFIAKEDSIYREQKSRMNGYNGQKEFKVVRKIEENKHITSFYLNTTDGS 180

Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG---GQVSNWLHN 235
            + E+ PGQY+ + L   G  H   R YSL+   + +  RI+VKRE G   G VSN+LH+
Sbjct: 181 GLPEFTPGQYISLTLSIPGTDHLHTRNYSLSDYGNKEALRISVKRESGKYKGLVSNYLHD 240

Query: 236 HANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHA 295
               GD++ L  P+G+F++  ++  P+  ++AGVG TP+++M  +L   G   ++ +   
Sbjct: 241 QVGEGDILSLGMPSGEFYLN-SNKGPLVFLAAGVGITPLISMYKSL--KGSEREIVFVQC 297

Query: 296 AENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDP 355
           A+N + HAF +E++   Q     T+   Y +P   D     FD +G +    L       
Sbjct: 298 AKNSESHAFRNEIE--SQKTDNVTSVVIYEEPLSND----IFDFKGYLTSKVLNDILPSS 351

Query: 356 TMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396
               Y+CGP  FM +    L +   K  ++H+E FGP + L
Sbjct: 352 PSDVYMCGPKSFMAYALDLLKEHEGKISDVHFEFFGPKEEL 392


Lambda     K      H
   0.318    0.135    0.404 

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: 391
Number of extensions: 20
Number of successful extensions: 6
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: 396
Length of database: 402
Length adjustment: 31
Effective length of query: 365
Effective length of database: 371
Effective search space:   135415
Effective search space used:   135415
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: 50 (23.9 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