GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Dinoroseobacter shibae DFL-12

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q5P171
         (474 letters)



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

 Score =  405 bits (1041), Expect = e-117
 Identities = 210/466 (45%), Positives = 288/466 (61%), Gaps = 4/466 (0%)

Query: 8   INGKPVRAGSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLM 67
           ING  V +  +F+V NPAT EV A         V+QA+AAA+AA PGW+     ER   +
Sbjct: 23  INGALVDSAGSFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGAYI 82

Query: 68  HALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPVEVIQD 127
            A   AL+AH  EL+ L+T E GKP   +    +  EV  AI W    A   L  EVI+D
Sbjct: 83  AAYADALDAHKQELITLLTTEQGKPRHSM----ATTEVEYAIFWVREVAKRRLEDEVIED 138

Query: 128 NDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRFVE 187
             +  ++V   PLGVVG+ITPWN+P+++ +W + P L  GNT+V+KPS  TP  T+RF E
Sbjct: 139 TPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFGE 198

Query: 188 LANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTLEL 247
           +A  + P GVLN+V G +  G+ + +HPDI KI FTGST TG+ +M +++ NLKR+TLEL
Sbjct: 199 IAQQVFPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRITLEL 258

Query: 248 GGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAKET 307
           GGND  I+LP  D K + P LF   + N+GQ C  +KRLYVH+S+Y+    +    A E 
Sbjct: 259 GGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFVAHAAEK 318

Query: 308 VVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIADA 367
            VG+G+   T+LGP+QNK Q   +++L  D +A G  +  GG+   G G F   T++ + 
Sbjct: 319 TVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPITIVDNP 378

Query: 368 KDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLECG 427
               RVV EE FGP+LP+I++SD++EV+  AN+ E GL  S+W  D   A  +A RLE G
Sbjct: 379 PKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVANRLEAG 438

Query: 428 TAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473
           T WVNE      D PFGG KQSG+GVE G+ GL+E+T+ +T    K
Sbjct: 439 TVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTKTYMFRK 484


Lambda     K      H
   0.317    0.136    0.405 

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: 694
Number of extensions: 31
Number of successful extensions: 2
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: 474
Length of database: 484
Length adjustment: 34
Effective length of query: 440
Effective length of database: 450
Effective search space:   198000
Effective search space used:   198000
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 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