GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Dinoroseobacter shibae DFL-12

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Dino:3607842
          Length = 351

 Score =  309 bits (791), Expect = 9e-89
 Identities = 180/372 (48%), Positives = 238/372 (63%), Gaps = 26/372 (6%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           M+ + L    K Y G+T+  V   +L I D EF VFVGPSGCGK+T LRMIAGLE+ +EG
Sbjct: 1   MSGITLRGAVKRY-GETQ-VVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
           +++IG R V  + P +R +AMVFQ YALYPHMTV +NM FGLK+  VPKAEI  +V  A+
Sbjct: 59  SIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAAS 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           +IL +   L RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV+MR EI +
Sbjct: 119 EILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LH+ +  T+IYVTHDQ EAMT+ D+IVV+R G ++Q   P  +Y  P N+FVAGFIGSPA
Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPA 238

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGK--PVVLGVRPEDLHDEEV 298
           MNF+ G I  + DA +         LP      L   GA G+  PV +GVRP     + +
Sbjct: 239 MNFLDGRI--ENDAVHLAG------LPP-----LPVPGAAGRSGPVTVGVRP-----QHI 280

Query: 299 FMTTYPDSVLQMQVEVVEHMGSEVYLH-TSIGPNTIVARVNPRHVYHVGSSVKLAIDLNK 357
            +    D  L   VE+ E +G   YL+      + +            G+ V L++  ++
Sbjct: 281 ALEPGGDGYL---VELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPVGLSLAPDR 337

Query: 358 IHIFDAETEESI 369
           + +F+AET + +
Sbjct: 338 VMLFEAETGQRL 349


Lambda     K      H
   0.321    0.138    0.395 

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: 394
Number of extensions: 14
Number of successful extensions: 1
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: 384
Length of database: 351
Length adjustment: 30
Effective length of query: 354
Effective length of database: 321
Effective search space:   113634
Effective search space used:   113634
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