GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK1 in Pseudomonas fluorescens GW456-L13

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate PfGW456L13_1897 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= TCDB::Q9X103
         (369 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1897 Glucose ABC
           transporter, ATP-binding subunit (EC 3.6.3.-)
          Length = 386

 Score =  349 bits (895), Expect = e-101
 Identities = 186/368 (50%), Positives = 248/368 (67%), Gaps = 13/368 (3%)

Query: 3   MAQVVLENVTKVYENKVV-AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDG 61
           MA + L NV K Y   +   +KN  L ++D EF++L+GPSGCGK+T +  IAGLE I+ G
Sbjct: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60

Query: 62  KIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAA 121
            I +D   ++ + PKDRDIAMVFQ+YALYP M+V +N+AFGLK+RK P  EID  V   +
Sbjct: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120

Query: 122 KILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKK 181
           K+L IE+LL RKP QLSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDAKLRV+MR+E+K 
Sbjct: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 182 LHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPP 241
           +H RL+ T +YVTHDQ+EAMT+ DK+ VMKDG IQQ GTP +IYN+PAN+FVA FIGSPP
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240

Query: 242 MNFVNARVVRGEGGL--WIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFAL 299
           MNF+  R+ R +G L   + +   + ++P   +D  A   D+E+I GIRPE I      L
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQD--AGLEDREVILGIRPEQI-----IL 293

Query: 300 APSPEN---TITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTR 356
           A    N   TI   V V EP G +T++ V + D  +   + P       + + L  D  +
Sbjct: 294 ANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAK 353

Query: 357 MHAFDKET 364
           +  FD +T
Sbjct: 354 VLLFDAKT 361


Lambda     K      H
   0.319    0.138    0.387 

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: 396
Number of extensions: 16
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: 369
Length of database: 386
Length adjustment: 30
Effective length of query: 339
Effective length of database: 356
Effective search space:   120684
Effective search space used:   120684
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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