GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pontimonas salivibrio CL-TW6

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_104913141.1 C3B54_RS02765 aldehyde dehydrogenase

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



>NCBI__GCF_002950575.1:WP_104913141.1
          Length = 507

 Score =  347 bits (889), Expect = e-100
 Identities = 200/483 (41%), Positives = 275/483 (56%), Gaps = 15/483 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           +I  ++ +      F  +SP   +   ++    +EDID A++AA AA   +W  +    R
Sbjct: 23  WIGGQWTKPVKGNYFEDISPVNGKPFCEIARGTAEDIDAALDAAHAAA-PAWGKASTTER 81

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142
             VL K+AD+ID + + LA  E  DNGK +  +   D+ L A +FR          G   
Sbjct: 82  AAVLNKIADVIDANVEMLAVAETWDNGKPIRETLNADIPLAADHFRYFVAAVRAQDGDFQ 141

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E       Y   EP+GV GQIIPWNFP+LMA+WKL P L  G   VLK AE TP S L L
Sbjct: 142 EMDGDTTAYHYHEPLGVVGQIIPWNFPILMAAWKLAPALSAGNAVVLKPAEQTPASILVL 201

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
           A LI +   PPGV+N+V+GFG  AG P++S P+I+K+AFTG T TGR I++ A+ +N+  
Sbjct: 202 AELIGDI-LPPGVLNIVNGFGAEAGKPLASSPRIRKIAFTGETTTGRLILQYAS-ANIIP 259

Query: 263 VTLELGGKSPNIVFDDA-----DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317
            TLELGGKSPNI FDD      D     Q       +N GEVC   SR  +Q+  YD  +
Sbjct: 260 TTLELGGKSPNIFFDDVSQEKDDFYDKAQEGFVLFAFNQGEVCTCPSRALIQKSHYDSFL 319

Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG---- 373
            +     +    G+P   DT +GAQ S  QL+KIL YIDIGK+EGAT++ GG+R      
Sbjct: 320 GDAVERTKKAIQGNPLDTDTQVGAQASNDQLEKILSYIDIGKQEGATLVCGGDRVDLGGD 379

Query: 374 -NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432
              GY+++P IF +     ++ ++EIFGPVV +T F   ++ I +AND+ YGL AGV + 
Sbjct: 380 LADGYYVEPAIF-EGNNKMRLFQEEIFGPVVAVTSFDDYDDAIQIANDTLYGLGAGVWSR 438

Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492
           N +TA      I +G +WVN Y+ +     FGGY  SGIGRE  + AL +Y Q K + + 
Sbjct: 439 NGNTAYRAGRDIQAGRVWVNNYHAYPAGAAFGGYKSSGIGRENNKLALSHYQQTKNLLVS 498

Query: 493 LSQ 495
            S+
Sbjct: 499 YSE 501


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: 642
Number of extensions: 33
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: 507
Length adjustment: 34
Effective length of query: 461
Effective length of database: 473
Effective search space:   218053
Effective search space used:   218053
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 24 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