GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Pseudomonas fluorescens FW300-N2C3

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 AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05180
          Length = 386

 Score =  345 bits (886), Expect = e-100
 Identities = 183/365 (50%), Positives = 248/365 (67%), Gaps = 7/365 (1%)

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

Query: 62  KIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAA 121
            I I  + V+ + PKDRDIAMVFQ+YALYP M+V EN+ FGLK+RK  +  ID  V   A
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120

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

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

Query: 242 MNFVNARVVRGEGGL--WIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFAL 299
           MNF+  R+ R +G L   + +   + ++P   +D  A   D+E+I G+RPE I   L   
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQD--AGLEDREVILGMRPEQI--MLAGS 296

Query: 300 APSPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHA 359
            P+   TI   V V EP G +T++ V + D  +   + P    +  + + L  D +++  
Sbjct: 297 EPNGLPTIRAEVQVTEPTGPDTLVFVSLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLL 356

Query: 360 FDKET 364
           FD ++
Sbjct: 357 FDAQS 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: 381
Number of extensions: 11
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:

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