GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas stutzeri RCH2

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF2231 Psest_2276 NAD-dependent aldehyde dehydrogenases

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__psRCH2:GFF2231
          Length = 506

 Score =  347 bits (890), Expect = e-100
 Identities = 199/482 (41%), Positives = 285/482 (59%), Gaps = 17/482 (3%)

Query: 22  GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81
           G +I  EFV     + F   SP   E I +   + +EDI+ A++AA AA   +W  +  Q
Sbjct: 20  GNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKALDAAHAAA-DAWGKTSVQ 78

Query: 82  VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGS 140
            R  +L K+AD I+ + + LA  E  DNGK++  +   DV L A +FR  AG     +GS
Sbjct: 79  DRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGS 138

Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200
             E  +    Y   EP+GV GQIIPWNFPLLMA+WKL P L  G   VLK AE TPLS +
Sbjct: 139 AAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIM 198

Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260
               ++ +   PPGV+N+V GFG  AG  +++  +I K+AFTGST  G HIM+ AAE N+
Sbjct: 199 VFIEVVGDL-LPPGVLNIVQGFGREAGQALATSTRIAKIAFTGSTPVGSHIMRCAAE-NI 256

Query: 261 KKVTLELGGKSPNIVFDD------ADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314
              T+ELGGKSPNI F+D      A ++   + LV   F+N GEVC   SR  +QE I++
Sbjct: 257 IPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLA-FFNQGEVCTCPSRALIQESIFE 315

Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG----- 369
             +       +++K G+P   DT +GAQ S+ Q DKIL Y++I ++EGA ++TGG     
Sbjct: 316 PFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQEGAQILTGGAAEKL 375

Query: 370 ERFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429
           E   + GY+++PT+     +  ++ ++EIFGPVV +  FK   E +A+AND+E+GL AGV
Sbjct: 376 EGSLSTGYYVQPTLIKGHNK-MRVFQEEIFGPVVGVATFKDEAEALAIANDTEFGLGAGV 434

Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
            T +++ A  +   I +G +W N Y+ +     FGGY +SG+GRE  +  LD+Y Q K +
Sbjct: 435 WTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNL 494

Query: 490 RI 491
            I
Sbjct: 495 LI 496


Lambda     K      H
   0.316    0.133    0.389 

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: 626
Number of extensions: 25
Number of successful extensions: 7
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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