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_104914315.1 C3B54_RS06570 NAD-dependent succinate-semialdehyde dehydrogenase

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



>NCBI__GCF_002950575.1:WP_104914315.1
          Length = 497

 Score =  272 bits (696), Expect = 2e-77
 Identities = 155/480 (32%), Positives = 258/480 (53%), Gaps = 10/480 (2%)

Query: 20  PTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS--WST 77
           PTGLFI+ E++++  +     ++PS + EIT+V +        A+EA  AA  S+  W  
Sbjct: 18  PTGLFIDGEWLRTGQE--IPVINPSDKSEITKVADGSG---GHALEALAAADRSAQQWRH 72

Query: 78  SDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKI 137
             P+ R  + +    L+ E AD  A +  +++GK    + G+  L+A +F   A     +
Sbjct: 73  WAPRARADLFHLAHGLLIERADAFADVMTMESGKPRAEALGEFNLSAGFFLWYAEQVAHL 132

Query: 138 KGSVIETGDTHFNYTR-REPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTP 196
            G   E     +      +P+G    + PWNFP+LM++ K G  L  GCT V+K+A  TP
Sbjct: 133 HGRYQEGSPGGYRVIETHQPVGPSFLVTPWNFPMLMSARKAGAALAAGCTVVIKSARETP 192

Query: 197 LSALYLASLIKEAGAPPGVVNVV-SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAA 255
           L+A      ++EAG P GVVN++ +         I +  ++KKV+FTGS+A G  ++K A
Sbjct: 193 LTAALFIDTLQEAGFPAGVVNLIHTSNSAEVSEQIMADSRLKKVSFTGSSAVGTVLLKQA 252

Query: 256 AESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDK 315
           +   +   ++ELGG  P IV DDADV   ++  V   F N G+ C A +RI + E I ++
Sbjct: 253 SNLIINS-SMELGGDGPFIVLDDADVDLAVREAVICKFRNAGQACVAANRIILHESIAEE 311

Query: 316 IVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK 375
              +F  A  +LK+GD F  +  +G   ++ QL+++   ++  +  G T++ GG     +
Sbjct: 312 FTEKFLAATAALKVGDGFDPEVSVGPIITERQLNRVSGLVESFQSAGGTLLAGGNVIDGE 371

Query: 376 GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLS 435
           G+F +PT+F     DH    DE+F P+  +    TV+E +  AND+ YGL+A V + +LS
Sbjct: 372 GFFFEPTVFRFDSYDHDFCNDELFAPIAALYTVTTVDEALRFANDTHYGLSAYVFSKDLS 431

Query: 436 TAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495
             ++V+ +++ G + VN      P  PFGG  +SG+GRE G E +  + + K + + + +
Sbjct: 432 RVVTVAERLDFGMVGVNRGIMSDPKAPFGGIKESGLGREAGHEGIYEFLEPKYIALTIDE 491


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: 557
Number of extensions: 22
Number of successful extensions: 5
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 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