GapMind for catabolism of small carbon sources

 

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

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q88RC0
         (480 letters)



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

 Score =  294 bits (752), Expect = 5e-84
 Identities = 173/463 (37%), Positives = 253/463 (54%), Gaps = 10/463 (2%)

Query: 15  INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74
           ING  +D+    + +V NPAT EV+   P     +  +AI AA  A P W AL+  ER A
Sbjct: 23  INGALVDSAG--SFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGA 80

Query: 75  KLRRWFELMIENQDDLARLMTTEQGKPL-AEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133
            +  + + +  ++ +L  L+TTEQGKP  + A  E+ YA   I W  E AKR   D +  
Sbjct: 81  YIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYA---IFWVREVAKRRLEDEVIE 137

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

Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253
           E+A +   PAGVL+VV G   E G  LT +  + K+SFTGST  GR++M   + ++K+++
Sbjct: 198 EIAQQV-FPAGVLNVVAGG-NEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRIT 255

Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313
           LELGGN P I+    D    +     + Y N+GQ C+   R+YV + +YD F     A  
Sbjct: 256 LELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFVAHA 315

Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE--GNFFEPTIL 371
           A+  +GNG++  T  GP+ +     K+++   D  ++G  V  GG++ +  GNF   TI+
Sbjct: 316 AEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPITIV 375

Query: 372 VDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEAL 431
            + PK + V +EE FGP+ P+ ++ D  EV+  +NDTEFGLA+  +  D      VA  L
Sbjct: 376 DNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVANRL 435

Query: 432 EYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
           E G V +N   I     PFGG K SG+G E  + G++++   K
Sbjct: 436 EAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTK 478


Lambda     K      H
   0.317    0.134    0.384 

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: 598
Number of extensions: 29
Number of successful extensions: 4
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: 480
Length of database: 484
Length adjustment: 34
Effective length of query: 446
Effective length of database: 450
Effective search space:   200700
Effective search space used:   200700
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 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, 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