GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc04256 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)

Query= reanno::Smeli:SMc04256
         (361 letters)



>lcl|FitnessBrowser__Miya:8501226 DvMF_1960 putrescine/spermidine
           ABC transporter ATPase protein (RefSeq)
          Length = 399

 Score =  205 bits (522), Expect = 1e-57
 Identities = 116/318 (36%), Positives = 174/318 (54%), Gaps = 33/318 (10%)

Query: 4   VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63
           + +R ++  F     LD ++L I +GEFL LLG SGCGK+T+L  ++G    + G++ I 
Sbjct: 8   IELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRIN 67

Query: 64  DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123
            + V    P+ R +  VFQ+YAL+P MTV  N++FGLK+  +   E  +RV  A  ++ +
Sbjct: 68  GQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHL 127

Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183
           +    RKP +LSGGQ+QRVAI RA++ +  V L DEP S LD KLR ++++EIK L + L
Sbjct: 128 ENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQL 187

Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI--------- 234
             T ++VTHDQ EA  ++DR+ VM  G I+Q+  P  IY  P N++VA F+         
Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGDINALPGR 247

Query: 235 ---------------------GSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRL 273
                                G+P       +++P +       GG  F V    +  RL
Sbjct: 248 IDAVRLDWSAAPGTPLAPPAPGTPEHAALPPDLKPGEHLYDATVGGTVFPVR---SRRRL 304

Query: 274 QPGQKVVLGLRPEHVKVD 291
            PG  V + LRPE +++D
Sbjct: 305 APGDGVQVLLRPEDLRID 322


Lambda     K      H
   0.320    0.137    0.392 

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: 372
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 361
Length of database: 399
Length adjustment: 30
Effective length of query: 331
Effective length of database: 369
Effective search space:   122139
Effective search space used:   122139
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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