GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3786
          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 (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