GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagP in Shewanella amazonensis SB2B

Align N-acetylglucosamine porter, NagP (characterized)
to candidate 6936374 Sama_0562 glucose/galactose transporter (RefSeq)

Query= TCDB::Q8EBL0
         (435 letters)



>lcl|FitnessBrowser__SB2B:6936374 Sama_0562 glucose/galactose
           transporter (RefSeq)
          Length = 413

 Score =  183 bits (465), Expect = 8e-51
 Identities = 141/425 (33%), Positives = 213/425 (50%), Gaps = 51/425 (12%)

Query: 8   QKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALP 67
           Q    L    + +LFFI GF T LN  L+P+LK I  L+  QA L+ F F+ A    +  
Sbjct: 18  QSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPL 77

Query: 68  SAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNP 127
           +  +I ++GY  G+  G+  M    LLF PA+  + +ALFL A  V+ +G T+LQ + NP
Sbjct: 78  AGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANP 137

Query: 128 YVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANG 187
           +V RLGPE +AA+R+++   LN     + PL  S LI   F    GT             
Sbjct: 138 FVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLI---FGAAAGT----------HEA 184

Query: 188 LVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVLALFV 247
           + LPYL +A  IGI+A+        ++ + D   DH  K  +   LSH  L LG LA+F+
Sbjct: 185 VQLPYLLLAAVIGIIAVGFIFLG-GKVKHADMGVDHRHKGSL---LSHKRLLLGALAIFL 240

Query: 248 YVAVEVIAGDTIGTFALSL-------GIDHYGV--MTSYTMVCMVLGYILGILLIPRVIS 298
           YV  EV    +IG+F ++        G+D      + S+     ++G   G  L  R  +
Sbjct: 241 YVGAEV----SIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRR-FN 295

Query: 299 QPTALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVW 358
               L  +A+   LL +              L +V  G +A    L+ +  +G  N+I++
Sbjct: 296 PAMVLAANAVFANLLLM--------------LTIVSSGELA----LVAVLAVGFFNSIMF 337

Query: 359 PAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLF 418
           P ++ LA+ G+G+LTS GS LL   I GGA  PV  G++  A ++G Q  ++V   CY +
Sbjct: 338 PTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVV--ADNVGVQLSFIVPTFCYFY 395

Query: 419 ILFYA 423
           I +YA
Sbjct: 396 ICWYA 400


Lambda     K      H
   0.326    0.141    0.414 

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: 520
Number of extensions: 32
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: 435
Length of database: 413
Length adjustment: 32
Effective length of query: 403
Effective length of database: 381
Effective search space:   153543
Effective search space used:   153543
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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