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

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources