GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Marinobacter adhaerens HP15

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  344 bits (883), Expect = 2e-99
 Identities = 178/377 (47%), Positives = 253/377 (67%), Gaps = 16/377 (4%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           M+++ L  I KTYPG  E T+K  ++DI   EF + VGPSGCGK+T +  IAGLE IT+G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
           ++ +  + ++ + PKDRDIAMVFQ+YALYP M+V +N+AFGLK+R +PK EID+ V+  A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
            +L I+ L+++KP  LSGGQ+QRVA+GRA+ R P+++L DEPLSNLDAKLRV+MR EI+K
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LHQRL+TT++YVTHDQ EAMT+ DRI V++DG +QQ  TP+ VY +P+N+FVAGF+GSPA
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 241 MNFI-----RGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL-- 293
           M+F+     +GE     +       S+ L +PE        +  +GK V+LG+RPE +  
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPE------FLADRVGKKVILGIRPEHITQ 294

Query: 294 -HDEEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLA 352
             D++   T       +  +EV E  G +V     +    +  R++P H    G + +L 
Sbjct: 295 PQDQKNDQTLVAKG--EFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELM 352

Query: 353 IDLNKIHIFDAETEESI 369
            D+ K+  FD ETE+ I
Sbjct: 353 FDMKKVVFFDPETEKRI 369


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: 420
Number of extensions: 15
Number of successful extensions: 3
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: 372
Length adjustment: 30
Effective length of query: 354
Effective length of database: 342
Effective search space:   121068
Effective search space used:   121068
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 (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