GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Halioglobus japonicus S1-36

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_102106082.1 C0029_RS01630 aldehyde dehydrogenase family protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>NCBI__GCF_002869505.1:WP_102106082.1
          Length = 474

 Score =  288 bits (738), Expect = 2e-82
 Identities = 161/467 (34%), Positives = 255/467 (54%), Gaps = 12/467 (2%)

Query: 14  FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           +I+G WVD    +++ V NPAT ++   +    AA+  +A +AA+ A  ++   + +ER 
Sbjct: 8   YINGEWVDPVEPKSMDVINPATEKVCARISIGSAADVDKAAKAANAAFASFSRTSREERV 67

Query: 74  TKLRRWYELIIENQDDLARLMTLEQGKPLA-EAKGEIVYAASFIEWFAEEAKRIYGDVIP 132
             L    E+  +  +D+A  +T E G P A     +       +    E  K    +   
Sbjct: 68  ELLGAICEVYQKRYNDIADAITEEMGAPTALSVHAQAATGIGHLSTAMEILKTFEFEEAA 127

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192
           GH       V K+PIGV   ITPWN+P   IT K GPALA GCT+VLKP+   P   +  
Sbjct: 128 GHSR-----VFKEPIGVCGMITPWNWPINQITCKVGPALAVGCTVVLKPSEVAPLCGYIF 182

Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV 252
           AE+   AG+PAGVF++++G    +G+ ++S+P++  +SFTGST  G  +    A  +K+V
Sbjct: 183 AEVMHEAGVPAGVFNMINGDGAGVGTAISSHPLIEMVSFTGSTRAGSLVAQNAAPSVKRV 242

Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVA 312
           + ELGG +P I+ DD +L++AV   ++  ++N GQ+C   +R+ +     +  A     A
Sbjct: 243 TQELGGKSPNILLDDVNLEEAVTRGVMHMFQNTGQSCNAPSRMLVPRAKMEEAAAIAANA 302

Query: 313 VAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAG--GKPM---EGNFFE 367
            A + +G+    GT+ GP++ E    K+Q  I   + +GA +  G  G+P    +G F +
Sbjct: 303 AATVVVGDPRAEGTSMGPVVSEVQWNKIQGLIQAGIDEGAVLACGGVGRPEGIDKGYFVQ 362

Query: 368 PTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRV 427
           PT+ +NV N+  +A+EE FGP+  +  +    + IA++NDT +GLA Y    D+ +V  V
Sbjct: 363 PTVFSNVNNDMTIAREEIFGPVLCIMPYDSLDEAIAIANDTPYGLAGYVQGEDMDQVMSV 422

Query: 428 AEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
           A  +  G + +N G   + + PFGG K SG GRE   +G  DYLEIK
Sbjct: 423 AGKIRAGNININ-GQSGDLMTPFGGYKQSGNGREWGAHGFTDYLEIK 468


Lambda     K      H
   0.317    0.135    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: 524
Number of extensions: 19
Number of successful extensions: 5
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: 474
Length adjustment: 33
Effective length of query: 447
Effective length of database: 441
Effective search space:   197127
Effective search space used:   197127
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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