GapMind for catabolism of small carbon sources

 

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

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  365 bits (938), Expect = e-105
 Identities = 209/483 (43%), Positives = 289/483 (59%), Gaps = 20/483 (4%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           +I  ++   V    F  ++P  G+V  + A   KED++ AV AA  AF+    W +  ++
Sbjct: 17  YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT---WSKTSST 73

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +LN++A  +E +  YLAA+ET+DNGK    +   DL + +   RY+AG      G 
Sbjct: 74  ERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGS 133

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              +D +  S   HEP+GV  QIIPWNFPLLM  WKL PALA GN VV+K AE TP++ +
Sbjct: 134 LSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIM 193

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +  LI +   PPGVVN+V GFG   G A+ ++  V K AFTGST  GR++   A + N+
Sbjct: 194 VLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYA-TENI 251

Query: 280 KRVTLELGGKSPNIIMS------DADMDWAVEQA-HFALFFNQGQCCCAGSRTFVQEDIY 332
             VTLELGGKSPNI  S      DA +D AVE A  FAL  NQG+ C   SR  +QEDIY
Sbjct: 252 IPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL--NQGEICTCPSRLLIQEDIY 309

Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGI-- 390
           ++F+ + + R K+  +G+P D     G Q  + QF+KI  YI  GK+EGA++L GG I  
Sbjct: 310 EKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE 369

Query: 391 ---AADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447
                  GY+I+PT+F    + M I +EEIFGPV+ +  FKT+EE +  AN++ YGL A 
Sbjct: 370 LPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAG 428

Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507
           V+T+D  +   + +A+QAG VWVN Y  + A +PFGGYK SG GRE  +  L  Y + K 
Sbjct: 429 VWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKN 488

Query: 508 VTV 510
           + +
Sbjct: 489 MLI 491


Lambda     K      H
   0.319    0.136    0.409 

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: 618
Number of extensions: 34
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: 517
Length of database: 501
Length adjustment: 34
Effective length of query: 483
Effective length of database: 467
Effective search space:   225561
Effective search space used:   225561
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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