GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Marinobacter adhaerens HP15

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF2761 HP15_2705 inner-membrane translocator

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Marino:GFF2761
          Length = 335

 Score =  148 bits (374), Expect = 2e-40
 Identities = 102/350 (29%), Positives = 177/350 (50%), Gaps = 22/350 (6%)

Query: 107 FLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGY 166
           F++  L  L++  +++V +    G+  + +    Q+ I      GLN++VG AG + LG+
Sbjct: 5   FMQSRLRGLVILALILVILPAFLGNPFHYE-LVTQMAIIAATVVGLNLLVGFAGQISLGH 63

Query: 167 VAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFG 226
             F+ +GAY   + +  +G S    L +  I       I+G P+LRL+G YL++ TLA G
Sbjct: 64  AGFFGLGAYFTGIATGTYGWSSVPALVVGAIVVGAIAWIVGRPILRLKGHYLSMATLAVG 123

Query: 227 EIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYL 286
            II ++L N   +T G  G+  +P   +FG  ++ +A G   LF + I         +Y+
Sbjct: 124 FIIAIILNNERALTGGPDGMP-VPAFEIFG--WELSAFGRYSLFGITIEGFQ----AWYI 176

Query: 287 ILALCMLTA-YVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFA 345
             ++ +L A +  + L   PIGRA  ++   E+A   +G+NT   K   F   A++A   
Sbjct: 177 FASVVLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTAKYKSLVFVISAIYASLM 236

Query: 346 GSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLK 405
           GS +A  QGF++P    F  S + + +VVLGGMGS  G+ + A+V+    ++L +   L+
Sbjct: 237 GSLYAHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGAVVLKLLPQVLADFQELE 296

Query: 406 LIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRERKAISG 455
            +             +FGL +++ M+F P+G + +       + RK   G
Sbjct: 297 HV-------------MFGLILMLTMIFMPKGLLPTLTAFVSKKMRKKAGG 333


Lambda     K      H
   0.330    0.145    0.432 

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: 473
Number of extensions: 29
Number of successful extensions: 5
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: 463
Length of database: 335
Length adjustment: 31
Effective length of query: 432
Effective length of database: 304
Effective search space:   131328
Effective search space used:   131328
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 (21.8 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