GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1141
          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:

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