Alignments for a candidate for Dshi_1194 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Pseudomonas putida KT2440

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate PP_3955 PP_3955 permease

Query= uniprot:E4PQE4
         (729 letters)



>FitnessBrowser__Putida:PP_3955
          Length = 675

 Score =  347 bits (889), Expect = 1e-99
 Identities = 224/647 (34%), Positives = 338/647 (52%), Gaps = 62/647 (9%)

Query: 115 ALYVLYQTFSFWQMVQNGAMRIPVE-LEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVP 173
           AL+ +   FS +Q+       I  + L   H G+ LL      + +S+     R  +   
Sbjct: 18  ALFAVALVFSVFQIATAAFPLISTQVLRAIHVGFLLLV-----VYLSYSFVGHRRPWQPL 72

Query: 174 DLVLIVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALV 233
             +L +  +A AAY        ++ S   + + + +    I    L+ E  RRV G+AL 
Sbjct: 73  AWLLGLAGMATAAYQWYFEGDLIQRSGELTTSDLIVGLLLIG---LVFEAARRVMGIALP 129

Query: 234 IIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQV-YTDAGILGPTTAVSSTYIILFIIFA 292
           II  +FLAY   G +LPG L + G  + +  +Q+ +   G+ G  T VS+TYI LFI+F 
Sbjct: 130 IICALFLAYGLLGQHLPGELAHRGYGLDQIVNQLAFGTEGLYGTPTYVSATYIYLFILFG 189

Query: 293 AFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLM 352
           AFL+ + +   F +FA    G   GGPAKVS+F+S LMG I G+   NVV+TG  TIPLM
Sbjct: 190 AFLEQAGMIRLFTDFAMGLFGHRSGGPAKVSVFSSALMGTITGSGVANVVTTGQFTIPLM 249

Query: 353 KKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFAS 412
           K+ GY    AG VEA +S G Q+MPP+MGA AFIMAE   +PY E+A AA+IPA+LYF S
Sbjct: 250 KRFGYKPAFAGGVEATSSMGSQLMPPVMGAVAFIMAETINVPYAEVAKAALIPALLYFGS 309

Query: 413 VYFMVDFEAAKTGMRGMREDELPKLRTMMKQ-CYLFVPIIILIVALFMGYSVIRAGTLAT 471
           VY+MV  EA ++ + G+  ++ P     ++Q  +L VP+++L+  LF G + + +G +  
Sbjct: 310 VYWMVHLEARRSHLHGLPREQCPSAWDALRQRWFLLVPLMVLVALLFSGRTPLYSGMVGL 369

Query: 472 VSAAVV------------SWLSPN-------------KMGLRHIL--------------- 491
              A+V            +WL                +MG+  IL               
Sbjct: 370 ALTAIVILGSAIILRAQKTWLRAAFWVALGILCSGFFRMGIGVILMVIAGLAIACCFVQG 429

Query: 492 ---------QALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLA 542
                     AL   +  A+ + + CA  GVI+GVISLTG+   F+  +LD+   +  L+
Sbjct: 430 GRATLHACVMALAEGARHAVPVGIACALVGVIIGVISLTGLATTFAGYILDLGRDNLFLS 489

Query: 543 LIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVA 602
           L+  M   ++LGMG+PT   Y + +S+ AP L++LG+  + +H FVFYF +++ +TPPVA
Sbjct: 490 LVLTMLTCLVLGMGIPTIPNYIITSSIAAPALLELGVPLIVSHMFVFYFGILADLTPPVA 549

Query: 603 LASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEA-GWFEIARALVTATF 661
           LA +AAA I+    +  S  + RI +A F+VPFM  Y+ AL+M+          ++ A F
Sbjct: 550 LACFAAAPIAKEKGLLISFWAVRIALAGFVVPFMAVYDPALMMQGDSMGSTLYMVIKAAF 609

Query: 662 GVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIAL 708
            V +     +G   +    W  RLL  AA + +I     +D  G AL
Sbjct: 610 AVALWGCASIGHLRA-PMPWWERLLAFAAGVSLILAAPISDEVGFAL 655


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: 1250
Number of extensions: 76
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: 675
Length adjustment: 39
Effective length of query: 690
Effective length of database: 636
Effective search space:   438840
Effective search space used:   438840
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 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources