GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3608018
          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 (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