GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malF1 in Pseudomonas stutzeri RCH2

Align MalF1; aka Maltose ABC transporter, permease 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 GFF850 Psest_0864 ABC-type sugar transport systems, permease components

Query= TCDB::Q9X0T0
         (577 letters)



>FitnessBrowser__psRCH2:GFF850
          Length = 521

 Score =  278 bits (710), Expect = 5e-79
 Identities = 195/562 (34%), Positives = 289/562 (51%), Gaps = 76/562 (13%)

Query: 10  WFLLAILNIALFWAGVFLFQNEYYELSIVLFSLLVLIDFFIINPRGYPYRYTIPALILLF 69
           W L    N    +  V L+  +    +++   +  +  +  IN R Y  RY  P++  + 
Sbjct: 30  WLLWLAFNALSLYLVVALYVQKQMAFALLGLVVTGIASYLFINRRMYAQRYIFPSVAGML 89

Query: 70  VLVLYPIYFTFKVAFTNYGTGHFMSRQEAIERLLYDPNFSYVVDSTPVSYKVFVVYDGLS 129
           V V++P+ +T  + FTNY   + +S Q  +ER        Y +  T ++ + F      S
Sbjct: 90  VFVIFPLLYTVGIGFTNYSGTNLLS-QAQVER--------YHLSQTYLAGERFRFTLHQS 140

Query: 130 PTDDFLILFKTGDTIFLGERPKPVVARGQEVLLSQFNLVPITGETISLNGDTFRIVPWPA 189
           P                GER +  V +G+   L  F   P+TGE              P 
Sbjct: 141 PD---------------GERLR--VDKGE---LGVFVSPPLTGE--------------PD 166

Query: 190 DLSEINLVVRGEKTYKSFYSPDDEILRLNAPYFKSRIAQGYLVNAEYVL--PDGKKLALR 247
             + ++L+            P + +  L        + Q   V  ++V+  PDG  L L 
Sbjct: 167 PEAPLSLL------------PAESVEGLGEALALREVIQRRKVLEQWVMQAPDGSLLRLY 214

Query: 248 IAPDGEWRFMYVERLYRLAYKEIYDGVKMKITTTVVNNLTGREVVEREGAFYDVDENGNE 307
               G      VE  YR       DG  + + T     LT     + E  FY VDE G +
Sbjct: 215 ----GLREVAAVEPQYR------QDGPGVLVETRTGARLTA----DMERGFY-VDETG-K 258

Query: 308 TFLVGFIDFVGWKNFLRIVKDPKVSGPFFRIFLWTFVWAVLSVVLSLAVGLPFALVLNNP 367
               GF  F G+ NF R++ +P +  PF +IF WTF +A L+VV +LAVGL  A +L   
Sbjct: 259 AVPPGFTVFTGFANFSRVLTEPSIREPFMQIFAWTFAFAGLTVVFTLAVGLVLASLLQWE 318

Query: 368 RLKGRNLYRTLLIIPWAIPVFISALVWRNGLLNESYGVINKFLLPLFGLEPIKWFNDPFW 427
            ++G+  YR +LI+P+A+P FIS LV+R GL N+++G IN  L  LFG+ P  WF+DP  
Sbjct: 319 LVRGKAFYRLMLILPYAVPGFISILVFR-GLFNQNFGEINLLLEGLFGIRP-DWFSDPSL 376

Query: 428 ARVGVLLVNVWLTFPYMMTISLGALQSIPPELYEVAAIDGAGRFRRFVHITFPLLMTIIA 487
           AR  +L+VN WL +PYM+ + +G LQ+IP + YE +AIDGA      + IT P L+  + 
Sbjct: 377 ARTMILIVNTWLGYPYMLLLCMGLLQAIPRDQYEASAIDGASPLDNLLRITLPQLIKPLM 436

Query: 488 PLLVSSFAFSFNNFTIIYLITGGGPPIPNSTTPTGYTDILISYVYKLAFEGGQGQDFGFA 547
           PLL++ FAF+FNNF +I L+T GGP I  +TTP G TD+L+SY Y++AF+   GQDF  A
Sbjct: 437 PLLIACFAFNFNNFVLITLLTRGGPDIIGATTPAGTTDLLVSYTYRIAFQ-DSGQDFALA 495

Query: 548 SAISILIFFLVGGISFVNFKLS 569
           +AI+ +IF LVG ++ +N KLS
Sbjct: 496 AAIATMIFILVGAMALLNLKLS 517


Lambda     K      H
   0.328    0.146    0.454 

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: 837
Number of extensions: 50
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 577
Length of database: 521
Length adjustment: 36
Effective length of query: 541
Effective length of database: 485
Effective search space:   262385
Effective search space used:   262385
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 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