GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_02292 H281DRAFT_02292 amino acid ABC transporter substrate-binding protein, PAAT family

Query= reanno::BFirm:BPHYT_RS07735
         (264 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02292 H281DRAFT_02292 amino
           acid ABC transporter substrate-binding protein, PAAT
           family
          Length = 264

 Score =  306 bits (783), Expect = 4e-88
 Identities = 150/258 (58%), Positives = 184/258 (71%), Gaps = 1/258 (0%)

Query: 8   IAALALFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKL 67
           + ALA   A+ A +  A AAD   + FG+EA Y PFESK P+GELQG DIDVGNAVC   
Sbjct: 7   LLALACAFASVAASSAAVAADTSTLRFGLEAQYPPFESKGPNGELQGLDIDVGNAVCVAA 66

Query: 68  KAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSG 127
              C WVE SFDGLIPALQ RKF+AINS M  TDQRRQ +DFT  +Y +P Q+IAK+ SG
Sbjct: 67  HMTCKWVETSFDGLIPALQGRKFDAINSAMNATDQRRQTIDFTTVVYRVPTQLIAKRDSG 126

Query: 128 LLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDAAFQD 187
           LLPTP +LKGK VGVLQ +IQET+AKA W PAGV VVPYQ Q+Q+Y DL +GRLDA    
Sbjct: 127 LLPTPEALKGKRVGVLQASIQETFAKAHWEPAGVTVVPYQDQNQVYTDLVAGRLDATLVL 186

Query: 188 AEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQALKELKADG 247
           A A   GFL KP G  + F G  V D+K+LG+G+ +G+RKGD AL++ LN A+ +++ADG
Sbjct: 187 APAGQTGFLSKPNGKDYAFVGQPVRDDKILGSGIAYGIRKGDTALRERLNAAIAKVQADG 246

Query: 248 TIDRFAAKYF-DVKVVLK 264
           T+   AAKY  D+ +  K
Sbjct: 247 TVKTLAAKYLGDIDISAK 264


Lambda     K      H
   0.317    0.133    0.383 

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: 221
Number of extensions: 6
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: 264
Length of database: 264
Length adjustment: 25
Effective length of query: 239
Effective length of database: 239
Effective search space:    57121
Effective search space used:    57121
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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, 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