GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Dinoroseobacter shibae DFL-12

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)

Query= reanno::MR1:200453
         (482 letters)



>lcl|FitnessBrowser__Dino:3608018 Dshi_1425 aldehyde dehydrogenase
           (RefSeq)
          Length = 484

 Score =  305 bits (781), Expect = 2e-87
 Identities = 183/467 (39%), Positives = 255/467 (54%), Gaps = 16/467 (3%)

Query: 15  INGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTAKERGA 74
           ING   D  S  +  + NPAT  V+A  P   + + + AIAAA+AA P W AL+  ERGA
Sbjct: 23  INGALVD--SAGSFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGA 80

Query: 75  KLRRWFELLNENSDDLALLMTSEQGKPL-TEAKGEVTYAASFIEWFAEEAKRIYGDTIPG 133
            +  + + L+ +  +L  L+T+EQGKP  + A  EV YA   I W  E AKR   D +  
Sbjct: 81  YIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYA---IFWVREVAKRRLEDEVIE 137

Query: 134 HQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALA 193
              +  + V   P+GV  AITPWNFP  +   K AP L  G TMV+KP+P TP   L   
Sbjct: 138 DTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFG 197

Query: 194 VLAERAGIPAGVFSVITGDAIAIGNE----MCTNPIVRKLSFTGSTNVGIKLMAQCAPTL 249
            +A++   PAGV +V+ G     GNE    +  +P + K+SFTGST  G K+MA  +  L
Sbjct: 198 EIAQQV-FPAGVLNVVAG-----GNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNL 251

Query: 250 KKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAEKL 309
           K+++LELGGN P I+    +    +     A Y N+GQ C+   R+YV   +YD+F    
Sbjct: 252 KRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDF 311

Query: 310 SMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHELGGNFFE 369
               A+  VG G+      GP+ N     K++    D   +G +V  GG++ +  GNF  
Sbjct: 312 VAHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVP 371

Query: 370 PTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLVWKV 429
            T++ N  K  RV REE FGP+ P+ K++D+D+V++ ANDTEFGLAA  +G D      V
Sbjct: 372 ITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGV 431

Query: 430 AESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476
           A  LE G V VN   I     PFGG K SG+G E  + G++E+   K
Sbjct: 432 ANRLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTK 478


Lambda     K      H
   0.318    0.133    0.390 

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: 575
Number of extensions: 29
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: 482
Length of database: 484
Length adjustment: 34
Effective length of query: 448
Effective length of database: 450
Effective search space:   201600
Effective search space used:   201600
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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