GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Burkholderia phytofirmans PsJN

Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00160 BPHYT_RS00160 ABC transporter substrate-binding protein

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



>FitnessBrowser__BFirm:BPHYT_RS00160
          Length = 262

 Score =  306 bits (785), Expect = 2e-88
 Identities = 152/256 (59%), Positives = 186/256 (72%), Gaps = 3/256 (1%)

Query: 1   MKMNWRNIAALALFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVG 60
           MK+    +A    FA+ +A++G +AA  ++   FG+EA Y PFESK P+GELQG DIDVG
Sbjct: 1   MKLLKPLLALACAFASLAASSGASAADTLR---FGLEAQYPPFESKGPNGELQGLDIDVG 57

Query: 61  NAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQM 120
           NAVC      C WVE SFDGLIPALQ RKF+AINS M  TD RRQA+DFT  +Y +P Q+
Sbjct: 58  NAVCVAAHMTCKWVETSFDGLIPALQGRKFDAINSAMNATDARRQAIDFTTVVYRVPTQL 117

Query: 121 IAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGR 180
           IAK+ SGLLPTPASLKGK VGVLQ +IQETYAKA W  AGV VVPYQ Q+Q+Y DL +GR
Sbjct: 118 IAKRDSGLLPTPASLKGKRVGVLQASIQETYAKAHWESAGVTVVPYQDQNQVYTDLVAGR 177

Query: 181 LDAAFQDAEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQAL 240
           LDA    A A   GFL KP G G+ F G  V D+K+LG+G+ +G+RKGD AL+D LN A+
Sbjct: 178 LDATLVLAPAGQTGFLSKPSGEGYAFVGEPVRDDKILGSGIAYGIRKGDTALRDRLNAAI 237

Query: 241 KELKADGTIDRFAAKY 256
            +++ADGT+   AAKY
Sbjct: 238 AKVQADGTVKTLAAKY 253


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: 230
Number of extensions: 5
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: 262
Length adjustment: 25
Effective length of query: 239
Effective length of database: 237
Effective search space:    56643
Effective search space used:    56643
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 (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:

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