GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutW in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for L-Histidine, permease component (characterized)
to candidate 351278 BT1750 glycine betaine/L-proline transport system permease (NCBI ptt file)

Query= reanno::pseudo5_N2C3_1:AO356_09615
         (283 letters)



>lcl|FitnessBrowser__Btheta:351278 BT1750 glycine betaine/L-proline
           transport system permease (NCBI ptt file)
          Length = 276

 Score =  256 bits (653), Expect = 5e-73
 Identities = 131/275 (47%), Positives = 188/275 (68%), Gaps = 1/275 (0%)

Query: 9   SIADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATR 68
           +I  ++   ++ L  ++   F  +S  +   I   + +L   P+++ +A++  +AW  + 
Sbjct: 3   NIGQYIETAINWLTEHFASFFDALSMGIGGFIDGFQHVLFGIPFYITIAVLAALAWFKSG 62

Query: 69  KVLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLM 128
           K  A   ++GLL + G +G W++ MQTLAL+L +T +++L+G+PLGI +A S+R   ++ 
Sbjct: 63  KGTAVFTLLGLLLIYG-MGFWEETMQTLALVLSSTCLALLLGVPLGIWTANSDRCNKIMR 121

Query: 129 PLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAI 188
           P+LD MQTMP+FVYLIP ++ FGLG VP  FAT+I+A PP++RLT LGIRQV   V+EA 
Sbjct: 122 PVLDFMQTMPAFVYLIPAVLFFGLGTVPGAFATIIFAMPPVVRLTGLGIRQVPKNVVEAS 181

Query: 189 NAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTL 248
            +FGA  WQ L+ VQLPLALP+I+ GINQT MM+LSMVVIA+MI A GLGE VL GI  +
Sbjct: 182 RSFGATPWQLLYKVQLPLALPTILTGINQTIMMSLSMVVIAAMISAGGLGEIVLKGITQM 241

Query: 249 NVGRGLEAGLAIVILAVVIDRITQAYGRPRHEVSK 283
            +G G E G+A+VILA+V+DRITQ     R    K
Sbjct: 242 KIGLGFEGGIAVVILAIVLDRITQGMADNRKSKKK 276


Lambda     K      H
   0.328    0.142    0.429 

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: 265
Number of extensions: 10
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: 283
Length of database: 276
Length adjustment: 26
Effective length of query: 257
Effective length of database: 250
Effective search space:    64250
Effective search space used:    64250
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: 47 (22.7 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, 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