GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Halopiger salifodinae KCY07-B2

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_049989147.1 LT39_RS03805 TRAP transporter large permease

Query= SwissProt::Q9HU16
         (427 letters)



>NCBI__GCF_000784335.1:WP_049989147.1
          Length = 431

 Score =  273 bits (699), Expect = 6e-78
 Identities = 154/431 (35%), Positives = 252/431 (58%), Gaps = 8/431 (1%)

Query: 1   MTILFLFLLLFLLMF-IGVPIAVSLGLSGALTILL----FSPDSVRSLAIKLFETSEHYT 55
           + ++ LF+L+ L ++ IGVP+A +LGL+  + +L     +SP+ V   A  L   ++ + 
Sbjct: 3   VVLIALFILVLLALYLIGVPVAFALGLTSLILMLTPMVSYSPELV---AQTLVSGADSFV 59

Query: 56  LLAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATV 115
           LLAIP FLL+G +M + G+   + DFA   +G IRGG+A   +LA +LF+ ++G++ A  
Sbjct: 60  LLAIPLFLLTGLYMNSFGLTSIIFDFAEEMIGPIRGGIAHVNILASILFSGMTGTAAADA 119

Query: 116 AAVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGV 175
           A +G+I    M  +GY + + A +  ++  +G +IPPS+ +++Y    + S+G LFIAG+
Sbjct: 120 AGLGAIEYEAMQDAGYEKGYSAAVTGSSAIIGPIIPPSVPLIMYGILAQVSIGVLFIAGI 179

Query: 176 VPGLLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAF 235
           VPGL++G  L+++    A           SL +   S + A   L   V+I+GG+  G F
Sbjct: 180 VPGLIMGATLLMLCTYYAHSHGYERGTWWSLPDIWESFKTAAPALGTPVLIIGGLLGGFF 239

Query: 236 TPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTE 295
           T TEA AVA  Y+ FV    Y  +   +  +   E    T  L FI+A+A L+  ++   
Sbjct: 240 TATEAGAVALFYTLFVGYVFYGGVENGDFVETTYEGVVTTAALTFIVASATLYGFLVRRA 299

Query: 296 QIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPI 355
           Q+P ++A  V  +   P + LL++  VLLI G  ME  A I IL P+F P+    GIDPI
Sbjct: 300 QLPDALAEAVIGVTGDPTLLLLMIVGVLLIVGLMMETIAAITILTPVFLPVIDVAGIDPI 359

Query: 356 HLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPA 415
           H GI+M++ + IGL+TPP G+ LF+   VT + L   +R+ +P+ + LL+ L++V  +P 
Sbjct: 360 HFGIVMILTLMIGLLTPPFGIILFILEKVTDVGLERIMRSMVPFYIPLLIILLLVVVLPG 419

Query: 416 VSLALPNWLGM 426
           ++L LP ++G+
Sbjct: 420 LTLWLPKFVGL 430


Lambda     K      H
   0.330    0.144    0.425 

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: 502
Number of extensions: 29
Number of successful extensions: 4
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: 427
Length of database: 431
Length adjustment: 32
Effective length of query: 395
Effective length of database: 399
Effective search space:   157605
Effective search space used:   157605
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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