GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate 209036 DVU0106 glutamine ABC transporter, permease protein

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>MicrobesOnline__882:209036
          Length = 223

 Score =  172 bits (435), Expect = 6e-48
 Identities = 93/216 (43%), Positives = 141/216 (65%), Gaps = 6/216 (2%)

Query: 1   MELDFSP--VWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYAL-CT 57
           M  DF P  +    P LLAG  +TV IT   L LG ++G + G+   N  R+  + +  T
Sbjct: 1   MAFDFQPQVMLDTAPLLLAGVKLTVLITLGGLALGFLLGAVAGLA--NSGRKAAFKVPAT 58

Query: 58  AYVAAIRGTPLLVQLFILFFGLP-QFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSID 116
            Y+ AIRGTPL+VQ+  L+FG+P   G+ +P    G++ + + SGAY++E+VRGAI SID
Sbjct: 59  IYIEAIRGTPLIVQVMFLYFGVPLATGMRIPPETAGILAIAVNSGAYIAEIVRGAIASID 118

Query: 117 KGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEG 176
            GQ EA RSIG++    M  ++ PQA  RMIPPLGN+FI  +K+++L+ ++ + +L  +G
Sbjct: 119 TGQSEAGRSIGLTRLQTMLYIIWPQAFRRMIPPLGNQFIISLKDTSLLVVIGVGELTRQG 178

Query: 177 QKIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIE 212
           Q+II+V++R+ EV+L +AV Y  +T +    LRR+E
Sbjct: 179 QEIIAVNFRAFEVWLTVAVFYLAMTLSIAWALRRLE 214


Lambda     K      H
   0.328    0.143    0.412 

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: 147
Number of extensions: 5
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: 222
Length of database: 223
Length adjustment: 22
Effective length of query: 200
Effective length of database: 201
Effective search space:    40200
Effective search space used:    40200
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 (21.8 bits)
S2: 45 (21.9 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