GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas fluorescens GW456-L13

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::Q4DRT8
         (561 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360
          Length = 496

 Score =  141 bits (355), Expect = 7e-38
 Identities = 136/452 (30%), Positives = 203/452 (44%), Gaps = 33/452 (7%)

Query: 83  ATPELAQKAIDTALQASRE--WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKS 140
           ATPE   +A+  A QA  +  W++T  R+R  +    A L+  +    L     L   KS
Sbjct: 52  ATPEDVDRAVLAARQAFDDSAWTRTRPRERQNLLWKLADLMQ-RDAELLAQLECLNNGKS 110

Query: 141 PFQAEIDVIAESCDFLRFSVHYAENLYRDQ-----PLSPSSGAVWNSLDYRPLEGFVSTI 195
              A++  +  + DFLR+   +A  +         PL P+    ++S   R   G V  I
Sbjct: 111 AAVAQVMDVQLAIDFLRYMAGWATKIEGSTVDVSAPLMPNDQ--FHSFIRREAVGVVGAI 168

Query: 196 APFNFAAIAANLVACPALM-GNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEP 254
             +NF  + A     PAL  G  V+ KP+    L+   L ++  EAG P GV N +    
Sbjct: 169 VAWNFPLLLACWKLGPALATGCTVVLKPADETPLTALKLAELVLEAGYPEGVFNVVT-GT 227

Query: 255 DVMTNFVNSHRDLAG-VAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHP 313
            +      +H  L   + FTGST V   I K          ++ R++ E GGK   +V  
Sbjct: 228 GITAGSALTHNPLVDKLTFTGSTAVGKQIGKIAMD------SMTRVTLELGGKSPTIVMA 281

Query: 314 SADLKLAAALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKS 373
            ADLK AAA      F  QGQ C A SRLY  +  ++ +   +  +   +K+G   D   
Sbjct: 282 DADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDNVVADISDIANAMKLGNGLDPSV 341

Query: 374 FMCAVIDETAFERNKKYIDIAKSSPSTYSVIAGGGYDKTEGWFVQPTIVESKDSQAQLMH 433
            M  +I     ER   YI+  + S +T   IA GG     G+FV+PT++   D +  L+ 
Sbjct: 342 DMGPLISARQQERVYGYIEKGRESGAT---IACGGEQFGPGFFVKPTVIVDVDQKHSLVQ 398

Query: 434 EEIFGPILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAA 493
           EEIFGP+L    +DD      +D   + N S  Y L  SI++ D  A+        R  +
Sbjct: 399 EEIFGPVLVAIPFDDE-----ADALRMANDS-PYGLGASIWSNDLAAVHRMIP---RIKS 449

Query: 494 GNYYINDKCTGAVVGQQPFGGARASGSNDKPG 525
           G+ ++N  C  A+    PFGG + SG   + G
Sbjct: 450 GSVWVN--CHSALDPALPFGGYKMSGVGREMG 479


Lambda     K      H
   0.320    0.133    0.402 

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: 569
Number of extensions: 26
Number of successful extensions: 3
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: 561
Length of database: 496
Length adjustment: 35
Effective length of query: 526
Effective length of database: 461
Effective search space:   242486
Effective search space used:   242486
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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