GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Marinobacter adhaerens HP15

Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= uniprot:A0A0D9B2B6
         (307 letters)



>lcl|FitnessBrowser__Marino:GFF3113 HP15_3056 high-affinity
           branched-chain amino acid ABC transporter, permease
           protein
          Length = 307

 Score =  404 bits (1038), Expect = e-117
 Identities = 197/307 (64%), Positives = 251/307 (81%)

Query: 1   MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL 60
           M D+ +F QQL+NGLT+GSTYALIAIGYTMVYGIIGMINFAHGE+YMIG+Y A IAI GL
Sbjct: 1   MQDLLYFSQQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGL 60

Query: 61  AMMGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120
           A +G+  +PL++  A + +++V+SS G+++ER+AYRP+RG +RLIPLISAIGMSIFLQN 
Sbjct: 61  AALGIAWLPLILIVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNY 120

Query: 121 VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG 180
           V L+Q S++   P LI G F  G G   ++ +SYMQI +F+ TL+ M  L+LFISRSR G
Sbjct: 121 VHLAQGSRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTG 180

Query: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK 240
           RACRA ++D+ MANLLGI+TN II+ TFVIGAALAA+A +LL M YG ++P  GF+ GLK
Sbjct: 181 RACRAVSQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLK 240

Query: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG 300
           AFTAAVLGGIGSIPGAMLGGL+LGVAE+  +     +YKDV++F LL+L+LLF+PTG+LG
Sbjct: 241 AFTAAVLGGIGSIPGAMLGGLILGVAESMTSGYLSGEYKDVISFSLLILILLFKPTGLLG 300

Query: 301 RPEVEKV 307
           +PEVEK+
Sbjct: 301 KPEVEKI 307


Lambda     K      H
   0.327    0.144    0.411 

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: 371
Number of extensions: 15
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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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 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