GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Psest_0084 in Marinobacter algicola DG893

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_050776516.1 MDG893_RS16430 TRAP transporter permease

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_000170835.1:WP_050776516.1
          Length = 660

 Score =  353 bits (906), Expect = e-101
 Identities = 206/553 (37%), Positives = 321/553 (58%), Gaps = 49/553 (8%)

Query: 217 TALIMELTRRVAGMALVIIGLVFLAYVFAGP---------YLPGFLGYPGLSVQRFFSQV 267
           T  ++E +RR  G  L +IG++ + Y  +G          +LPG L + G S+ R  +Q+
Sbjct: 108 TITLLEASRRAVGTGLTVIGVIAILYAMSGQRGPLSELGEWLPGILNHRGYSLDRIGAQL 167

Query: 268 YT-DAGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFA 326
           Y    GI G    V++T++ +F++F A L+ +  G +F++ AFAA GR RGGPAK ++ A
Sbjct: 168 YLGQEGIFGLPLGVAATFVFIFVLFGAMLEVTGAGRFFIDLAFAATGRQRGGPAKAAVLA 227

Query: 327 SGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFI 386
           S  MG I+G++  NVV+TG+ TIPLMKK+G+    AG +EAAASTGGQIMPP+MGAGAF+
Sbjct: 228 SASMGSISGSAIANVVTTGAFTIPLMKKLGFRPAQAGGIEAAASTGGQIMPPLMGAGAFL 287

Query: 387 MAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQ-CY 445
           +AE T +PY +I   ++ PA+LYFA+VY +V   A K GM+G+   +LP+LR +M    Y
Sbjct: 288 IAEYTRVPYLDIVKVSVFPALLYFATVYLLVHICAVKQGMKGLPASDLPQLREVMAYGWY 347

Query: 446 LFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWL-----------SPNKMG------LR 488
             +PII+L+  L MG S +R G  A V    ++ L           + N++G      LR
Sbjct: 348 FLLPIIMLVYLLVMGISPMRVGFYAVVGIIGIAGLNGLYLAYKQGRADNQLGKALTDALR 407

Query: 489 H----ILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALI 544
                +LQ LE+ +  A+ + + CA AG++V V+ LTG+G +FS +++  A  + L+AL 
Sbjct: 408 EGVVKLLQGLELGARNAVPVSIACAIAGIVVAVVGLTGLGLKFSSMMIAFADGNILMALF 467

Query: 545 FAMFISILLGMGMPTTAAYAVAASVVAPGLV-QLGIEPLTAHFFVFYFAVVSAITPPVAL 603
             +  S++LG+G+P TA+Y V   +V P L  + GI  L AH  VF+++  S +TPPVAL
Sbjct: 468 LVVIASLILGLGLPVTASYIVLIVLVGPALTNEFGIPLLVAHLLVFWYSQDSNVTPPVAL 527

Query: 604 ASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAG------WFEIARALV 657
           A++A A I+G+  METSV +++     +++P    +N  +++E G      W      L 
Sbjct: 528 AAFAGAAIAGSKTMETSVQAWKFAKGLYLIPLFMVFN-PVIIEGGPLPLVLWNGFIAILA 586

Query: 658 TATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQK 717
            A F     +  + G+  +    W+ RL L  A + +    L  ++ G+ +A+LA +   
Sbjct: 587 LAAF-----AAALEGFLFTHMKPWM-RLALSGAVIAIFYPDLQVEVAGV-VAMLALLAMN 639

Query: 718 --QRKTRLATAGA 728
              R+  L  AGA
Sbjct: 640 YWHRRRELHGAGA 652


Lambda     K      H
   0.327    0.139    0.410 

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: 1281
Number of extensions: 82
Number of successful extensions: 6
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: 729
Length of database: 660
Length adjustment: 39
Effective length of query: 690
Effective length of database: 621
Effective search space:   428490
Effective search space used:   428490
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: 54 (25.4 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