GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Pseudomonas fluorescens FW300-N2E2

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate Pf6N2E2_3298 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= uniprot:Q92L07
         (510 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3298
          Length = 481

 Score =  222 bits (566), Expect = 2e-62
 Identities = 147/445 (33%), Positives = 224/445 (50%), Gaps = 10/445 (2%)

Query: 44  IASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEA 103
           I       AA+    IE A  AF AW       R + +  +G E+ A + +LG+L++ E 
Sbjct: 34  IGEYAKADAAQVNAAIEAARAAFPAWSTSGIQARHDALDKVGSEILARREELGQLLAREE 93

Query: 104 GKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNF 163
           GK   E +GEV    +I  F  G   +L G  + + RPG  +  T   LGVVG+I+ +NF
Sbjct: 94  GKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPSVRPGVNVEVTREALGVVGLITPWNF 153

Query: 164 PVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIGD- 222
           P+A+ +W  A AL  G+ VV KP+E  P  A A   I+ RA       P G   +++G  
Sbjct: 154 PIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALAEIISRA-----GFPAGAFNLVMGSG 208

Query: 223 RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMA 282
           R +G++LV+ PKV  +S TGS  +GR++      R A+  LE+GG N  I+   ADL  A
Sbjct: 209 RVVGDILVNSPKVDGISFTGSVGVGRQIAVNCVSRQAKVQLEMGGKNPQIILDDADLKQA 268

Query: 283 LRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVD 342
           +      A  + GQRCT   RL V   ++D+ V  + +  QS+ VG+ L++   +GP+V 
Sbjct: 269 VELAVQSAFYSTGQRCTASSRLIVTAGIHDKFVAAMAERMQSIKVGHALKAGTDIGPVVS 328

Query: 343 KAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALVEMPKQEGPV-LEETFAPI 401
           +A      K I   ++ G  +  G  +      GY++ P L    +    +  EE F P+
Sbjct: 329 EAQLSQDLKYIDIGQSEGARLVSGGGLVTCDTEGYFLAPTLFADSEASMRISREEIFGPV 388

Query: 402 LYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEI 461
             V++ +D++A LA  N    GLS+ I T  ++ +  F     S  G+  VN+ T+G + 
Sbjct: 389 ANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHF--KRHSQAGMVMVNLPTAGVDY 446

Query: 462 GGAFGGEKETG-GGRESGSDAWKAY 485
              FGG K +  G RE G  A + Y
Sbjct: 447 HVPFGGRKGSSYGSREQGRYAQEFY 471


Lambda     K      H
   0.317    0.134    0.390 

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: 510
Number of extensions: 25
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: 510
Length of database: 481
Length adjustment: 34
Effective length of query: 476
Effective length of database: 447
Effective search space:   212772
Effective search space used:   212772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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