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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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