GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Marinobacter adhaerens HP15

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate GFF2761 HP15_2705 inner-membrane translocator

Query= uniprot:A0A159ZYE0
         (418 letters)



>FitnessBrowser__Marino:GFF2761
          Length = 335

 Score =  186 bits (473), Expect = 7e-52
 Identities = 110/317 (34%), Positives = 176/317 (55%), Gaps = 15/317 (4%)

Query: 94  IVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAY 153
           ++LALI+  ++  F G+    ++ T + I     +GLN++VG AG + LG+ GF+ +GAY
Sbjct: 14  VILALIL-VILPAFLGNPFHYELVTQMAIIAATVVGLNLLVGFAGQISLGHAGFFGLGAY 72

Query: 154 SYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRN 213
              + +  +G S    L +  ++     +++G P+LRL+G YL++ TL  G II + L N
Sbjct: 73  FTGIATGTYGWSSVPALVVGAIVVGAIAWIVGRPILRLKGHYLSMATLAVGFIIAIILNN 132

Query: 214 LTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEY--FGLEYNSINKVIFLYLVALL 271
              +TGGP+G+     P F    +E      L  F  Y  FG+           Y+ A +
Sbjct: 133 ERALTGGPDGMP---VPAFEIFGWE------LSAFGRYSLFGITIEGFQA---WYIFASV 180

Query: 272 LALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFF 331
           + L A++    L+  PIGRA  ++   E+A   +G+N    K   F + A +A   GS +
Sbjct: 181 VLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTAKYKSLVFVISAIYASLMGSLY 240

Query: 332 AARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMF 391
           A  QG +TP   +F  S + + +VVLGGMGS  GVIL A+V+ LLP+++ +F E   +MF
Sbjct: 241 AHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGAVVLKLLPQVLADFQELEHVMF 300

Query: 392 GALMVLMMIWRPQGLLP 408
           G +++L MI+ P+GLLP
Sbjct: 301 GLILMLTMIFMPKGLLP 317


Lambda     K      H
   0.331    0.145    0.439 

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: 479
Number of extensions: 29
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 418
Length of database: 335
Length adjustment: 30
Effective length of query: 388
Effective length of database: 305
Effective search space:   118340
Effective search space used:   118340
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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