GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Sphingomonas indica Dd16

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_085218595.1 B9N75_RS09590 aldehyde dehydrogenase family protein

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_900177405.1:WP_085218595.1
          Length = 479

 Score =  262 bits (669), Expect = 2e-74
 Identities = 169/457 (36%), Positives = 244/457 (53%), Gaps = 11/457 (2%)

Query: 28  IKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMIENQ 87
           ++VT+  TG+V   V +         I AA KA      + + ER A L+   +   E  
Sbjct: 23  LEVTDKYTGKVAFRVAQADAKTIDAGIAAAVKAAEPMARMASYERQAVLQHCVDRFTERF 82

Query: 88  DDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRL-----IV 142
           D+LA  +  E GKP+ +A+GE+          AEE+ R+ G+  P     KR      I 
Sbjct: 83  DELAYALCVEAGKPINDAEGEVTRLIDTFRIAAEESVRMTGEVQP-LDISKRARGYMGIW 141

Query: 143 IKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIP 202
            + PIG  + I+P+NFP  +   K  PA+A GC  V+KPAS+TP  A+ + E+     +P
Sbjct: 142 KRVPIGPCSFISPFNFPLNLAAHKIAPAIAVGCPFVMKPASRTPLGAIIMGEVLAETDLP 201

Query: 203 AGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAPF 262
            G  S++     E     T +  ++ LSFTGS  +G  L  +  K  KKV LELGGNA  
Sbjct: 202 KGAFSILPAHR-EGADMFTEDERLKLLSFTGSPGVGWDLKAKAGK--KKVVLELGGNAAV 258

Query: 263 IVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNGL 322
           IV  DADL+ AV   I   +  +GQ+C+   RI +   +YDA  EKLAA    L  G+  
Sbjct: 259 IVDKDADLEDAVARIIFGAFYQSGQSCIGVQRIIIHADIYDALKEKLAAKTKTLVAGDPH 318

Query: 323 EEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGNFFEPTILVDVPKTAAVAK 382
           +  T  GP+ID K   ++   I++AV  GAK+L GGK  +G   E T+L  V ++A V +
Sbjct: 319 DRKTFVGPMIDLKEATRLDNWIQEAVEGGAKLLVGGKR-DGAMLEATLLEGVDRSATVYR 377

Query: 383 EETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGIN-TG 441
           EE FGP+A L +F D A  +   ND++FGL +  + RD+ +V    + L+ G V IN   
Sbjct: 378 EEAFGPVAILSKFDDFAAALDEVNDSKFGLQAGIFTRDIFQVLNAWDRLDVGGVVINDVP 437

Query: 442 LISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCI 478
               +  P+GG+K SGLGREG ++ +ED  EI+ L I
Sbjct: 438 SYRVDNMPYGGVKDSGLGREGIRFAMEDMTEIRNLVI 474


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: 542
Number of extensions: 21
Number of successful extensions: 6
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: 479
Length adjustment: 34
Effective length of query: 446
Effective length of database: 445
Effective search space:   198470
Effective search space used:   198470
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