GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Klebsiella michiganensis M5al

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BWI76_RS05985 BWI76_RS05985 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQH9
         (318 letters)



>FitnessBrowser__Koxy:BWI76_RS05985
          Length = 349

 Score =  167 bits (424), Expect = 3e-46
 Identities = 114/331 (34%), Positives = 179/331 (54%), Gaps = 44/331 (13%)

Query: 7   VNILWLLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGH 66
           V I+  + LLAG ++        V N + ++++  I + +ILAV  NLI G +GQ SL  
Sbjct: 16  VIIVLCVALLAGINV--------VFNDYIIRVISTIFVFMILAVSYNLINGVTGQLSLEP 67

Query: 67  AGFMAIGAYAAAII-------------GSKSP----TYGAFFGAMLVGALLSGAVALLVG 109
            GF+A+GAY  A++              + SP     +  F  A+L+  L + A+A+ + 
Sbjct: 68  NGFVAVGAYVTALLILSSDSKLDMFEMAAPSPWILVLHAGFLPALLISGLCAAALAVCLA 127

Query: 110 IPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILGIP---NFTTWQMVYFFVVI 166
           +P  R++GDYLA+ TLG   II+I  IN   +TNGA G+  IP   +   W     F ++
Sbjct: 128 LPVFRVRGDYLAIVTLGFGFIIKILAINNPQITNGAIGLNDIPQQPHLLFW--CGLFALL 185

Query: 167 TTIATLNFLRSPIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFI 226
            T   L  + S  GR   +VR+DE AA ++GVNT +IK  AF   A    I G L A  +
Sbjct: 186 ATGMILQLVWSKYGRMMKAVRDDEDAAIAMGVNTFRIKTCAFATSAFFEGIGGGLLASLL 245

Query: 227 GSVVPKDYTFINSINVLIIVVFGGLGSITGAIVSAIV-------LGILNMLLQ----DVA 275
            ++ P  + F+ +  +LII+V GGLGS TGA++  ++       L  L+  LQ    D+ 
Sbjct: 246 TTISPGLFDFMLTFQLLIIIVLGGLGSTTGALLGTVLVVGSGEWLRFLDQPLQFFGHDLG 305

Query: 276 S---VRMIIYALALVLVMIFRPGGLLGTWEL 303
           +   +RM++++L L+++M+F   GLLG  E+
Sbjct: 306 AYPGLRMVVFSLLLLIIMLFAREGLLGKKEI 336


Lambda     K      H
   0.327    0.143    0.403 

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: 221
Number of extensions: 13
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: 318
Length of database: 349
Length adjustment: 28
Effective length of query: 290
Effective length of database: 321
Effective search space:    93090
Effective search space used:    93090
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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