GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagP in Shewanella loihica PV-4

Align N-acetylglucosamine transporter nagP (characterized)
to candidate 5208608 Shew_1119 glucose/galactose transporter (RefSeq)

Query= reanno::ANA3:7025962
         (432 letters)



>FitnessBrowser__PV4:5208608
          Length = 418

 Score =  728 bits (1878), Expect = 0.0
 Identities = 370/418 (88%), Positives = 388/418 (92%), Gaps = 1/418 (0%)

Query: 15  MAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRK 74
           MAIVA LFFILGFATWLNGSLMPYLKQILQL P QASLILFSFYIAVTFTALPSAWVIRK
Sbjct: 1   MAIVAGLFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRK 60

Query: 75  VGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPYVVRLGP 134
           VGYK GMA+GMGIMM+AGLLFIPAAKTQ+F LFL AQLVMGTGQTLLQTAVNPYVVR+GP
Sbjct: 61  VGYKTGMAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGP 120

Query: 135 EESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANSLVFPYLG 194
           EESAAARVSVMGILNKGAGVIAPLVF+ALILDSFKDR+G  LTQ QIDEMAN LVFPYLG
Sbjct: 121 EESAAARVSVMGILNKGAGVIAPLVFTALILDSFKDRVGVELTQAQIDEMANGLVFPYLG 180

Query: 195 MAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVIALFVYVAVEVI 254
           MAIFIGVLAL VKKSPLPEL NEDE  E T KG  + ALSHPNLA GV+ALF YVAVEVI
Sbjct: 181 MAIFIGVLALLVKKSPLPELENEDEQEEGT-KGHTREALSHPNLALGVVALFFYVAVEVI 239

Query: 255 AGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTALMISAILGLLLT 314
           AGDTIGTFALSLGVE+YGVMTSYTM+CMV+GY+LGI+ IPRFISQP ALMISAILGL+LT
Sbjct: 240 AGDTIGTFALSLGVENYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISAILGLMLT 299

Query: 315 LAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWPLALSGLGKLTS 374
           L ILFGDN SYAIANALLVPFGG  LPDTLL IAFLGLANAIVWPAVWPLALSG+GKLTS
Sbjct: 300 LGILFGDNESYAIANALLVPFGGAMLPDTLLMIAFLGLANAIVWPAVWPLALSGMGKLTS 359

Query: 375 TGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYAVKGHKMRHW 432
           TGSALL+MGIAGGAFGPLFWGLTSSAT +GQQGGYMVMLPCYLFILFYAVKG+KMR W
Sbjct: 360 TGSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYAVKGYKMRSW 417


Lambda     K      H
   0.327    0.141    0.421 

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: 839
Number of extensions: 38
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: 432
Length of database: 418
Length adjustment: 32
Effective length of query: 400
Effective length of database: 386
Effective search space:   154400
Effective search space used:   154400
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: 51 (24.3 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