GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Desulfovibrio vulgaris Miyazaki F

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 8501089 DvMF_1825 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__Miya:8501089
          Length = 339

 Score =  208 bits (529), Expect = 2e-58
 Identities = 109/303 (35%), Positives = 179/303 (59%), Gaps = 8/303 (2%)

Query: 16  RVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKD 75
           R   +V AV+ +S+ +  GE+L +VGESG GKS    +++ L    G    GE ++ G+ 
Sbjct: 37  RKRTVVHAVNDVSFDILPGETLSVVGESGCGKSTLARTVIGLYRATG----GEILYRGER 92

Query: 76  LLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL-MKNEEARERAIE 134
           +  L+   +   R + + ++FQ+P  SLNP ++V   + EP+ +H   + + + R R  +
Sbjct: 93  IDNLSDNGMLPYRTR-MQMVFQDPYASLNPRMKVREILEEPVRFHNPGISDADVRARVAD 151

Query: 135 LLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIM 194
           ++E+VG+  +P   + YP +FSGG RQR+ IA AL   P+ ++ADEP +ALDV+IQAQ++
Sbjct: 152 VMEQVGV--NPLWGVRYPHEFSGGQRQRISIARALVVDPEFIVADEPISALDVSIQAQVL 209

Query: 195 ELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGL 254
            L+ +++E+  ++ +FI+HDLSV  +   R+  MY G + E A  E++   P HPYT+ L
Sbjct: 210 NLMMDMQEKRNLTYLFISHDLSVVEHISTRVAVMYLGSLCELASAEDLFGNPRHPYTRAL 269

Query: 255 LNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNISENHRV 314
           L++   IG +    + + G+ P P   P+GC FH RC  A   C +E P    +    +V
Sbjct: 270 LSAIPRIGGKAAGHIKLSGDVPTPINLPTGCVFHGRCQHANARCMQEVPKARQLEGGAQV 329

Query: 315 ACH 317
           ACH
Sbjct: 330 ACH 332


Lambda     K      H
   0.320    0.139    0.401 

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: 281
Number of extensions: 13
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: 324
Length of database: 339
Length adjustment: 28
Effective length of query: 296
Effective length of database: 311
Effective search space:    92056
Effective search space used:    92056
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: 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