GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)

Query= BRENDA::Q70HW1
         (384 letters)



>lcl|FitnessBrowser__Dino:3608008 Dshi_1416 ABC transporter related
           (RefSeq)
          Length = 347

 Score =  320 bits (821), Expect = 3e-92
 Identities = 178/365 (48%), Positives = 226/365 (61%), Gaps = 22/365 (6%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA + L H+ K +       V+DF+L I D+EF V +GPSGCGKTTT+RMIAGLE+ + G
Sbjct: 1   MAEIRLNHVQKRWGSFVG--VEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            ++IGDR VN + PKDRD+AMVFQ+Y LYP+M VY+N+ F LK+RKVP+ E + RV  A+
Sbjct: 59  EIWIGDRMVNALDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEARVMRAS 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
            ++++   L RKP ALSGGQRQRVAL RAIVREP VFLMDEPLSNLDAKLRV  RA+I+ 
Sbjct: 119 AMVELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKN 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           L   LQ T IYVTHDQ EAMT+ DR+VVM  GV+QQ  TP  +Y +P N FVA FIGSPA
Sbjct: 179 LSHELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFIGSPA 238

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300
           MN + G  V DG                 R  +   SGA G+ V LG R ED        
Sbjct: 239 MNLMEG-AVTDG------------TFHGDRVAIAGLSGAAGR-VTLGFRAEDA------Q 278

Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHI 360
               D  +   V  +E +G    +    G   +  +        +G+ V++ I     H+
Sbjct: 279 VVDSDGQIAAPVYSMELLGDATMVTVKAGGTLVAVKAPKEFRAEIGAPVQIRIPTGICHL 338

Query: 361 FDAET 365
           FDA+T
Sbjct: 339 FDAQT 343


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: 415
Number of extensions: 12
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: 384
Length of database: 347
Length adjustment: 30
Effective length of query: 354
Effective length of database: 317
Effective search space:   112218
Effective search space used:   112218
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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