GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_4867 PP_4867 branched-chain amino
           acid ABC transporter, periplasmic amino acid-binding
           protein (braC-like)
          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 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