GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_1194 in Nocardiopsis lucentensis DSM 44048

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_017598723.1 D471_RS33945 TRAP transporter large permease subunit

Query= uniprot:E4PQE4
         (729 letters)



>NCBI__GCF_000341125.1:WP_017598723.1
          Length = 455

 Score =  154 bits (389), Expect = 9e-42
 Identities = 133/425 (31%), Positives = 198/425 (46%), Gaps = 85/425 (20%)

Query: 371 TGGQIMPPIMGAGAFI------MAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKT 424
           T G ++ P++   A +      M    G   T +AI  +   IL    + +  D E  + 
Sbjct: 10  TRGYLIAPVVAIFALLSMGFSPMFSAMGAVVTTVAINVLTQYIL----MPWRRDEETGEL 65

Query: 425 GMRGMREDELPKLRTMMKQCYLFVPIIILIVA---LFMGYSVIRAG-------------- 467
             R  R+   P +R       L +PII+  VA   L M    + AG              
Sbjct: 66  KTRSGRDITSPAVR-------LPLPIIVAAVAATVLVMVGQWVMAGMDRGMVALATTLLL 118

Query: 468 TLATVSAAVV--SWLSP--NKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGV 523
           TLA ++ AV    W     +++ L   L  L  A+ +AI IIV CA+AGVI GVI+ T +
Sbjct: 119 TLAGIAVAVAFGRWRESGEDQLNLHSFLDGLVGAARLAIPIIVACASAGVIAGVITTTDL 178

Query: 524 GARFSVLLLDVA--------------ATSQLLA-----------------------LIFA 546
           G + S  LL +A              A S +LA                       L  +
Sbjct: 179 GLKLSDGLLGIAESISSGLASLLTAVAASPVLAWTGAGADFGATAVGTLRVDLFLILFMS 238

Query: 547 MFISILLGMGMPTTAAYAVAASVVAPGLV---QLGIEP-----LTAHFFVFYFAVVSAIT 598
           M   ++LG+G+PTTA Y + A++ AP +V   Q  ++      L AH FV+YF V++ IT
Sbjct: 239 MIACLILGIGLPTTANYVITATLAAPAIVAVLQGSVDERLAMLLMAHLFVYYFGVLADIT 298

Query: 599 PPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLM-EAGWFEIARALV 657
           PPV LA+YAA+GISG + + T   S RI IAAF++P+MF ++  LL+ E  W     A +
Sbjct: 299 PPVCLAAYAASGISGGDPIRTGFYSVRIAIAAFVMPYMFVFSPELLLQEVNWLTGTIAAI 358

Query: 658 TATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQK 717
           T   G  M++ G++G +     +W  R+ LI   LL++ G L  +  G+ L V     +K
Sbjct: 359 TGVAGAVMVALGLVG-YVDRPLAWYKRVGLIVGGLLLVSGSLVANAVGLVLIVAVLGYEK 417

Query: 718 QRKTR 722
            R  R
Sbjct: 418 LRTRR 422



 Score = 37.0 bits (84), Expect = 2e-06
 Identities = 77/336 (22%), Positives = 133/336 (39%), Gaps = 57/336 (16%)

Query: 434 LPKLRTMM-KQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVS---------WLSPN 483
           LP LR +M  + YL  P++ +   L MG+S + +   A V+   ++         W    
Sbjct: 1   LPTLRRLMITRGYLIAPVVAIFALLSMGFSPMFSAMGAVVTTVAINVLTQYILMPWRRDE 60

Query: 484 KMGLRHILQALEIAS---YMAIQIIVVCAAAGVIVGVISLT------GVGARFSVLLLDV 534
           + G        +I S    + + IIV   AA V+V V          G+ A  + LLL +
Sbjct: 61  ETGELKTRSGRDITSPAVRLPLPIIVAAVAATVLVMVGQWVMAGMDRGMVALATTLLLTL 120

Query: 535 AATSQLLA-----------LIFAMFISILLG---MGMPTTAAYA---VAASVVAPGLVQL 577
           A  +  +A           L    F+  L+G   + +P   A A   V A V+    + L
Sbjct: 121 AGIAVAVAFGRWRESGEDQLNLHSFLDGLVGAARLAIPIIVACASAGVIAGVITTTDLGL 180

Query: 578 GIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMF 637
            +            + ++++   VA +   A   +GA+   T+V + R+ +  F++ FM 
Sbjct: 181 KLSDGLLGIAESISSGLASLLTAVAASPVLAWTGAGADFGATAVGTLRVDL--FLILFMS 238

Query: 638 FYNGALLMEAGWFEIARALVTATFG----VYMLSGGV------------LGWFASISASW 681
                L++  G    A  ++TAT      V +L G V              ++  + A  
Sbjct: 239 MI-ACLILGIGLPTTANYVITATLAAPAIVAVLQGSVDERLAMLLMAHLFVYYFGVLADI 297

Query: 682 ITRLLLIAAALLMIEGG--LWTDLTGIALAVLAFVI 715
              + L A A   I GG  + T    + +A+ AFV+
Sbjct: 298 TPPVCLAAYAASGISGGDPIRTGFYSVRIAIAAFVM 333


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: 827
Number of extensions: 47
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 729
Length of database: 455
Length adjustment: 36
Effective length of query: 693
Effective length of database: 419
Effective search space:   290367
Effective search space used:   290367
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 Apr 09 2024. 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