GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Marinobacter adhaerens HP15

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF3355 HP15_3297 binding-protein-dependent transport systems inner membrane component

Query= TCDB::Q9KKE2
         (285 letters)



>FitnessBrowser__Marino:GFF3355
          Length = 344

 Score =  218 bits (555), Expect = 1e-61
 Identities = 112/238 (47%), Positives = 166/238 (69%), Gaps = 8/238 (3%)

Query: 43  IEWILRGL-------PWWLVILAFMALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQT 95
           + W L G        PWW+VI   +A+    ++ W L L V   +  +  +  +D  MQT
Sbjct: 95  LSWFLDGALYAMLNTPWWIVIPLLLAVVYVVTKSWKLMLFVGGSIVLLAFIDHYDYAMQT 154

Query: 96  LALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKV 155
           LA++ +   + V++GVP+GI +A+S  ++ + +PVLD++QT+P FVYLIP + LF + + 
Sbjct: 155 LAIIFVCAFLCVLLGVPIGIAMARSNSLQRMIIPVLDMLQTLPPFVYLIPLIFLFSVTES 214

Query: 156 PAI-LATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATPTIMAG 214
               +A I+YA+ P+IRLT+LGIR VD +V+EAA AFG +P Q L+ V++PLA P IMAG
Sbjct: 215 KLYGIAIILYAIVPVIRLTNLGIRLVDKDVIEAADAFGMTPRQKLYKVQIPLALPNIMAG 274

Query: 215 LNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLDRITQ 272
           +NQTIMM+L+MVV+AS++ A GLG  VL GI+ L++G GL +G+GIVILAV+LDR+T+
Sbjct: 275 VNQTIMMSLAMVVIASLVSAPGLGVLVLRGIRNLELGVGLVSGLGIVILAVILDRVTK 332


Lambda     K      H
   0.327    0.142    0.422 

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: 324
Number of extensions: 14
Number of successful extensions: 2
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: 285
Length of database: 344
Length adjustment: 27
Effective length of query: 258
Effective length of database: 317
Effective search space:    81786
Effective search space used:    81786
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 (21.7 bits)
S2: 48 (23.1 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