GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagP in Shewanella sp. ANA-3

Align N-acetylglucosamine transporter nagP (characterized)
to candidate 7025962 Shewana3_3110 glucose/galactose transporter (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7025962 Shewana3_3110 glucose/galactose
           transporter (RefSeq)
          Length = 432

 Score =  842 bits (2175), Expect = 0.0
 Identities = 432/432 (100%), Positives = 432/432 (100%)

Query: 1   MTLDKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIA 60
           MTLDKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIA
Sbjct: 1   MTLDKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIA 60

Query: 61  VTFTALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTL 120
           VTFTALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTL
Sbjct: 61  VTFTALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTL 120

Query: 121 LQTAVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQ 180
           LQTAVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQ
Sbjct: 121 LQTAVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQ 180

Query: 181 IDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAF 240
           IDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAF
Sbjct: 181 IDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAF 240

Query: 241 GVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQP 300
           GVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQP
Sbjct: 241 GVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQP 300

Query: 301 TALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPA 360
           TALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPA
Sbjct: 301 TALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPA 360

Query: 361 VWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFIL 420
           VWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFIL
Sbjct: 361 VWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFIL 420

Query: 421 FYAVKGHKMRHW 432
           FYAVKGHKMRHW
Sbjct: 421 FYAVKGHKMRHW 432


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: 897
Number of extensions: 31
Number of successful extensions: 1
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: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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