GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pedobacter sp. GW460-11-11-14-LB5

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

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



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  356 bits (914), Expect = e-103
 Identities = 208/481 (43%), Positives = 284/481 (59%), Gaps = 19/481 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           +I  +FV       F  +SP   +  T+   +  ED++ AV+AA  AF  +WS +    R
Sbjct: 17  YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAF-KTWSKTSSTER 75

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142
             +L K+A  ++++ + LA +E +DNGK++  +   D+ L   +FR  AG     +GS+ 
Sbjct: 76  SIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSLS 135

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E      +    EPIGV  QIIPWNFPLLM  WKL P L  G   VLK AESTP+S + L
Sbjct: 136 ELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMVL 195

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             LI +   PPGVVNVV+GFG   G  + ++PK+ K AFTGST TGR +M+ A E N+  
Sbjct: 196 MELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATE-NIIP 253

Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           VTLELGGKSPNI F      DDA +   ++  V     N GE+C   SR+ +QE IY+K 
Sbjct: 254 VTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVM-FALNQGEICTCPSRLLIQEDIYEKF 312

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGE------ 370
           +++     +++KIG P      MGAQ S++Q +KI  YI +GK+EGA V+TGGE      
Sbjct: 313 IAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPG 372

Query: 371 RFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVH 430
             G  GY+IKPTIF    +  +I ++EIFGPV+ +T FKTVEE I +AND+ YGL AGV 
Sbjct: 373 ELGG-GYYIKPTIFKGHNK-MRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVW 430

Query: 431 TTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVR 490
           T +      V   I +G +WVN Y+ +    PFGGY QSG+GRE  +  L +Y Q K + 
Sbjct: 431 TRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNML 490

Query: 491 I 491
           I
Sbjct: 491 I 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: 608
Number of extensions: 31
Number of successful extensions: 8
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: 501
Length adjustment: 34
Effective length of query: 461
Effective length of database: 467
Effective search space:   215287
Effective search space used:   215287
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.

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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