GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Marinobacter adhaerens HP15

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate GFF3112 HP15_3055 high-affinity leucine-specific leucine-specific-binding periplasmic protein of high-affinity branched-chain amino acid ABC transporter transport system periplasmic binding protein

Query= SwissProt::P21175
         (373 letters)



>lcl|FitnessBrowser__Marino:GFF3112 HP15_3055 high-affinity
           leucine-specific leucine-specific-binding periplasmic
           protein of high-affinity branched-chain amino acid ABC
           transporter transport system periplasmic binding protein
          Length = 370

 Score =  474 bits (1221), Expect = e-138
 Identities = 222/347 (63%), Positives = 289/347 (83%), Gaps = 1/347 (0%)

Query: 26  AADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQLEGVIYDDACDPKQA 85
           AA  I+I +AGP+TGPVAQYGDMQ +GA MAIEQIN  GGV G +L  V YDD CDPKQA
Sbjct: 24  AAAEIQIGIAGPMTGPVAQYGDMQFSGARMAIEQINANGGVMGEELVAVEYDDVCDPKQA 83

Query: 86  VAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTI 145
           V VAN +VNDGV+FV+GH+CSSSTQPA+DIYEDEG+LM+TP++T+PEIT RGY+L+FRTI
Sbjct: 84  VTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGILMVTPASTSPEITERGYELVFRTI 143

Query: 146 GLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAG 205
           GLD+MQGPVA ++IA +  ++ +A++HDKQQYGEGIAT V+ T++DAG+++A+FEG+ AG
Sbjct: 144 GLDSMQGPVAARYIASQNPER-VAIVHDKQQYGEGIATAVRDTLKDAGVEIAMFEGITAG 202

Query: 206 DKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAG 265
           DKDF++L++KLK+A V +VY+GGYHPE+GL+LRQA  A LDARFMGPEGVGN +I  IAG
Sbjct: 203 DKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQANSADLDARFMGPEGVGNKDINTIAG 262

Query: 266 DASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEAD 325
           +A+EG+L TLP AF+Q  +N+AL+ AF+ K +DPSG FVL +Y+AV ++A+GIE AG  D
Sbjct: 263 EAAEGLLVTLPPAFDQKAENQALVKAFEDKGEDPSGPFVLTSYTAVQLVAEGIEAAGSTD 322

Query: 326 PEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDATRTEV 372
           P  VA ALR  TF+TP G + +D+ GD+K+F+F VYEWH D ++T V
Sbjct: 323 PFDVAAALREGTFQTPIGTVEYDKAGDMKSFEFVVYEWHSDGSKTPV 369


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: 541
Number of extensions: 24
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: 373
Length of database: 370
Length adjustment: 30
Effective length of query: 343
Effective length of database: 340
Effective search space:   116620
Effective search space used:   116620
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.

Links

Downloads

Related tools

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 preprint 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