GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Williamsia sterculiae CPCC 203464

Align Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized)
to candidate WP_076476644.1 BW971_RS03485 aldehyde dehydrogenase family protein

Query= SwissProt::S0ENH1
         (461 letters)



>NCBI__GCF_900156495.1:WP_076476644.1
          Length = 480

 Score =  360 bits (923), Expect = e-104
 Identities = 187/464 (40%), Positives = 273/464 (58%), Gaps = 10/464 (2%)

Query: 6   FYNIITGQPRSARETTSGVNPLDRSSLWPAPVATGNDVEEAVRSAQEAFPAWSEKTYKQR 65
           + N+I G+ RS+ E+    NP         PVAT  D+++AV +A  A+P WS  +  +R
Sbjct: 9   YANVINGETRSSAESAPVYNPATGQVFAEVPVATRADLDDAVTAAAAAYPGWSATSAAER 68

Query: 66  TELLEKFADLYLVHANEFCQLIATECGRTAGNAAIEVYVAAQWLRYPSKYEIPEEVTEDE 125
              +    D    HA EF  L+  E G+    A  EVY +  W R  +K ++P+EV ED 
Sbjct: 69  AAAVSAIGDRLEAHAEEFITLLTAEQGKPRSMAEWEVYGSVAWFREIAKQQLPDEVVEDT 128

Query: 126 KKTSIVT-HEPLGVVAAICPWNFPLMLALGKIAPALATGNCVILKPSPFTPYSSLKLVEL 184
            +  +++ + PLGVV AI PWNFP++LA+ KIAPAL TGN +I+KPSPFTP   LKLVEL
Sbjct: 129 PERRVISRYTPLGVVGAIVPWNFPILLAVWKIAPALVTGNTIIVKPSPFTPLCDLKLVEL 188

Query: 185 AQQVFPPSVLQVLHGHDDLGPMLVKHPRIQKITFTGSTTTGKQILRDAAETMKRVTLETA 244
            Q + PP VL  L G DDLG  +  HP I KI FTGST TG+ ++  AA T+KRVTLE  
Sbjct: 189 VQDLLPPGVLSALSGDDDLGKWMTVHPGIAKIAFTGSTETGRHVMASAAGTLKRVTLELG 248

Query: 245 GNNASIILPDVNIEAVIPQLAGGLWFNAGQVCIATRRMYIHQDIFDEAVAQLAEASKDLA 304
           GN+ +I+L DV+ + V PQ+    + N  Q C A +R+YIH D++D    +L E ++ + 
Sbjct: 249 GNDPAIVLRDVDPQKVAPQIFWAAFQNNAQFCNAAKRIYIHDDVYDAVRDELVEYARSVV 308

Query: 305 SG--------MEPIQNEMQLVRLQQALSDANAAGCELLSLGKTEA-AEGFFIQPTILKSP 355
            G        + PIQN  QL ++ +   D    G      G+ +  +EG+F+  T++ +P
Sbjct: 309 VGDGSHPDTQLGPIQNRPQLAKVTEYFDDCRKNGYTFALGGEIDTESEGWFVPVTLVDNP 368

Query: 356 PPDADVVQQENFGPIVSCIKFSSLDEAISLANNSDTGLAASVWSSDVSAARRVAAKLEVG 415
           P D+ +V +E FGPI+  +K+S  D+ ++ AN++  GL A+VW  D+ A  R+  ++E G
Sbjct: 369 PEDSRLVAEEPFGPILPLLKWSEEDDVVARANDTVWGLGATVWGDDLEAVERIGRRIEAG 428

Query: 416 NVYINGPPQPDPYVPFGGHKQSGLGVEYGLPGLLSFCQTKSTYL 459
            V++N   Q  P+  FGGHKQSG+G E  L GL  +   ++  L
Sbjct: 429 TVWLNEVHQYSPHQVFGGHKQSGIGAENSLHGLAEYTNYQTVCL 472


Lambda     K      H
   0.316    0.132    0.392 

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: 529
Number of extensions: 26
Number of successful extensions: 3
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: 461
Length of database: 480
Length adjustment: 33
Effective length of query: 428
Effective length of database: 447
Effective search space:   191316
Effective search space used:   191316
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: 51 (24.3 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