GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Shewanella amazonensis SB2B

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 6937206 Sama_1376 methylmalonate-semialdehyde dehydrogenase (RefSeq)

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



>FitnessBrowser__SB2B:6937206
          Length = 497

 Score =  207 bits (526), Expect = 9e-58
 Identities = 142/474 (29%), Positives = 230/474 (48%), Gaps = 12/474 (2%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           +I+ EF   + ++     +P+  + I +V  A  E++  A+ +A AAF S W       R
Sbjct: 8   YIDGEFTTGQGERIITVTNPANNQPIAEVRCASDEEVHGAIASAKAAFQS-WKEVPVSER 66

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIE 143
            +V+ +   L+ EH D LA I A + GK+   +KGDV                + G  +E
Sbjct: 67  ARVMLRYQALLKEHHDELATILAKETGKTFEDAKGDVWRGIEVAEHACNIASLLMGETVE 126

Query: 144 TGDTHFN-YTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
                 + Y+  +P+GVC  I P+NFP ++  W     +  G T VLK +E  P++ L L
Sbjct: 127 NVARKIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAVACGNTFVLKPSEQDPMTPLRL 186

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
           A L ++AGAP GV+ +V G   +A   + +HP IK ++F GS   G+++ K   + NLK+
Sbjct: 187 AELFEQAGAPKGVLQLVHG-DKSAVDILLTHPDIKAISFVGSVGVGQYVYKTGTD-NLKR 244

Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322
           V    G K+  ++  DA+ +  I +LV       G+ C A S + V  G   + + E K 
Sbjct: 245 VQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMAIS-VAVFVGAAKEWIPELKE 303

Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGY----F 378
           A   ++ G    +D   G   S     ++LK I+ GK EGA  +  G  F   GY    +
Sbjct: 304 ALAKVRPGLWDDKDAGYGPLISPAAKARVLKLIEQGKAEGAECLLDGSDFTVPGYESGNW 363

Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438
           + PT+F  V  D  I ++EIFGPV+   +   +E+ I L N S YG    + T + + A 
Sbjct: 364 VGPTMFDKVTTDMSIYKEEIFGPVLCCMEVDELEDAIELVNKSPYGNGTSIFTASGAAAR 423

Query: 439 SVSNKINSGTIWVNTYNDFH-PMVPFGGYSQSGIGRE--MGEEALDNYTQVKAV 489
              ++I  G + +N       P   F G+  S  G +   G++A+  +T+ K +
Sbjct: 424 KYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAIRFFTETKTI 477


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: 562
Number of extensions: 25
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
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