GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Pseudomonas putida KT2440

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate PP_1141 PP_1141 branched-chain amino acids ABC transporter - periplasmic leucine binding subunit

Query= SwissProt::P21175
         (373 letters)



>lcl|FitnessBrowser__Putida:PP_1141 PP_1141 branched-chain amino
           acids ABC transporter - periplasmic leucine binding
           subunit
          Length = 371

 Score =  527 bits (1357), Expect = e-154
 Identities = 256/366 (69%), Positives = 305/366 (83%)

Query: 7   RLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGV 66
           ++S+LFAAM +AG AS+S AADTIKI +AGP TGPV QYGDMQ  GA  AI+ IN AGGV
Sbjct: 3   KISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVTQYGDMQFIGAKQAIKDINAAGGV 62

Query: 67  NGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITP 126
           +G  LE   YDDACDPKQAVAVANKVVNDGVKFVVGH+CSSSTQPA+DIYEDEGV+MITP
Sbjct: 63  DGKMLEAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMITP 122

Query: 127 SATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVK 186
           +AT+PEIT+RGYKLIFRTIGLD+ QGP AG +IA+  K K +AVLHDKQQYGEGIAT VK
Sbjct: 123 AATSPEITARGYKLIFRTIGLDSAQGPAAGNYIADHVKPKVVAVLHDKQQYGEGIATAVK 182

Query: 187 KTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLD 246
           +T+E  G KVAVFEGLNAGDKDF+++I KLK+  V FVY+GGYHPE+GL+LRQA++ GL 
Sbjct: 183 QTLESKGTKVAVFEGLNAGDKDFSSIIQKLKQNNVDFVYYGGYHPELGLILRQAQEKGLK 242

Query: 247 ARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLP 306
           A+FMGPEGVGN  I+ IA +ASEG+L TLP++F+ DP NK ++DA KA  +DPSG FV P
Sbjct: 243 AKFMGPEGVGNDSISQIAQNASEGLLVTLPKSFDADPANKKIVDAIKADGKDPSGPFVFP 302

Query: 307 AYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKD 366
           AYSAV +IA+GI+KAG  D +KVAEA+   TF+TPTG+L FD+KGDLK+F F VYEWH  
Sbjct: 303 AYSAVELIAQGIKKAGSDDTDKVAEAIHKGTFKTPTGDLSFDDKGDLKDFKFVVYEWHFG 362

Query: 367 ATRTEV 372
             +TEV
Sbjct: 363 KPKTEV 368


Lambda     K      H
   0.316    0.133    0.377 

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: 563
Number of extensions: 22
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: 373
Length of database: 371
Length adjustment: 30
Effective length of query: 343
Effective length of database: 341
Effective search space:   116963
Effective search space used:   116963
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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