GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natD in Pseudomonas stutzeri RCH2

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components

Query= TCDB::Q8YXD0
         (288 letters)



>lcl|FitnessBrowser__psRCH2:GFF3786 Psest_3855 Branched-chain amino
           acid ABC-type transport system, permease components
          Length = 295

 Score =  123 bits (308), Expect = 6e-33
 Identities = 82/282 (29%), Positives = 157/282 (55%), Gaps = 11/282 (3%)

Query: 7   QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFV-NTFGVNIWLSM 65
           QL++ G+  GS  A+ ++GL + +G+L++ NFAHG    +GA+  + +  T G+  W ++
Sbjct: 15  QLLI-GLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATLGIGYWPAL 73

Query: 66  IVA--VVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNY 123
           I+A  +VG    ++  E+L  SR+ ++  +    ++ + GLAL L       +G   Q Y
Sbjct: 74  ILAPIIVGLCSAVI--ERLALSRLYNL--DHLYSLLFTFGLALALEGAFRYFYGSSGQPY 129

Query: 124 NLP--ITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKV 181
            +P  +    ++  + +P+ +  V+  +++   A   L++ TK+G  +RA  ++  L + 
Sbjct: 130 AVPKELAGGYNLGFMFLPKYRAWVVLASLVICIASWLLIEKTKLGAYLRAATENPTLVRT 189

Query: 182 SGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGA 241
            GI+V  ++ +T+ +   +  L G +   I  V P MG  LI+ +FA V++GG+G+  GA
Sbjct: 190 FGINVPLLLTFTYGMGAALAGLAGMLAAPIYQVSPLMGSNLIIVVFAVVVVGGMGSILGA 249

Query: 242 IAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
           I   +++GI++ ++  F   +    V  +IM +VLL+RP GL
Sbjct: 250 IITGYMLGILEGLTKVFY-PEASNIVIFVIMAIVLLVRPAGL 290


Lambda     K      H
   0.328    0.144    0.426 

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: 225
Number of extensions: 13
Number of successful extensions: 2
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: 288
Length of database: 295
Length adjustment: 26
Effective length of query: 262
Effective length of database: 269
Effective search space:    70478
Effective search space used:    70478
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: 48 (23.1 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