GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Pseudomonas putida KT2440

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate PP_4867 PP_4867 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein (braC-like)

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__Putida:PP_4867
          Length = 378

 Score =  352 bits (904), Expect = e-102
 Identities = 188/370 (50%), Positives = 247/370 (66%), Gaps = 6/370 (1%)

Query: 3   YKLSLLVAVAATAM-TASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGV 61
           YK   L    ATA+  +S  +AD+ +  AGP+TG  A FGEQ  KG + A   INAAGGV
Sbjct: 6   YKKGFLALAVATALGVSSYVQADVKIGVAGPMTGANAAFGEQYMKGAQAAADKINAAGGV 65

Query: 62  LGQKLKLEVGDDACDPKQAVAVANQLAKAG-VKFVAGHFCSGSSIPASQVYAEEGVLQIS 120
            G+K+ L  GDDAC+PKQAVAVAN+L     V  V GHFCS ++IPAS+VY E GV+ I+
Sbjct: 66  NGEKIVLVKGDDACEPKQAVAVANRLVDQDKVIGVVGHFCSSNTIPASEVYDEAGVIAIT 125

Query: 121 PASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADET 180
           P STNP++TE+ L  +FR+CGRDDQQG +AG Y+++  KGK VA+LHDK  YG+GLAD T
Sbjct: 126 PGSTNPQVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVLHDKDTYGQGLADAT 185

Query: 181 QKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGL 240
           +  L   G K  +YE  T GEKD+SA+V+K++    DVVY GG H EAG L RQ+++QGL
Sbjct: 186 KAQLEKRGVKPVLYEGLTRGEKDFSAVVTKIRSTGADVVYFGGLHPEAGPLVRQLREQGL 245

Query: 241 -NAPIVSGDALVTNEYWAITGPAG--ENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGY 297
            +   +S D +VT+E  +  G A   +   MTFG DPR +P++K  VE+FRKAG EPEGY
Sbjct: 246 KDVKFMSDDGIVTDELVSTAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKAGTEPEGY 305

Query: 298 TLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRW 357
           TLY YA+LQ  A A   A S      A  L+ N   TV+G+  +D+KGD+T   YV Y+W
Sbjct: 306 TLYAYASLQALAAAFNGAKSNKGEDAAKWLKANPVQTVMGEKKWDSKGDLTVSDYVVYQW 365

Query: 358 N-NGQYAQVK 366
           +  G+Y Q++
Sbjct: 366 DKTGKYHQLE 375


Lambda     K      H
   0.312    0.129    0.366 

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: 439
Number of extensions: 16
Number of successful extensions: 3
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: 366
Length of database: 378
Length adjustment: 30
Effective length of query: 336
Effective length of database: 348
Effective search space:   116928
Effective search space used:   116928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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