GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Marinobacter adhaerens HP15

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase

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



>FitnessBrowser__Marino:GFF3684
          Length = 489

 Score =  302 bits (774), Expect = 1e-86
 Identities = 173/480 (36%), Positives = 269/480 (56%), Gaps = 17/480 (3%)

Query: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKE 71
           Q F+ G ++    G+T  V NPATG+++  V     +  + AIE+A      W A+TA E
Sbjct: 9   QNFVHGRFLANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIE 68

Query: 72  RATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYGDV 130
           R+  L R   ++ E  D+LA     + GKP  EA+  ++V  A  +E+FA  A  I    
Sbjct: 69  RSRILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSI---- 124

Query: 131 IPGHQPDKR---LIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPF 187
             G+Q D         ++P+G+ A I  WN+P  +   K+ PALA G  M+ KP+ +TP 
Sbjct: 125 -EGNQQDLGGDFYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPM 183

Query: 188 SAFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK 247
            A  LAE+   AG+PAGVF+VV G+A ++G  LT +P + K+SFTG    G+++M+  + 
Sbjct: 184 GAVKLAEIFTEAGVPAGVFNVVQGAA-EVGQWLTHHPEIAKVSFTGEVATGKKVMAAASS 242

Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307
            +K V++ELGG +P I+FDDADL+ A+  A++  +   G+ C    R+++ + +Y  F E
Sbjct: 243 TLKDVTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIE 302

Query: 308 KLKVAVAK-LKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPME---- 362
           +L       +K G+ +   T  G LI  K    V ++IA  LS+GAT+  GG+  E    
Sbjct: 303 RLLERTRNNIKPGDPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDS 362

Query: 363 --GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARD 420
             G F EPTI T+  ++  + KEE FGP+  +  F+DE +VIA +N+T+ GLA+  +  D
Sbjct: 363 KGGYFVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTND 422

Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480
           + R  RV   ++ G+  +N+   S    P GG K SG+GRE  +  I  Y +IK + +G+
Sbjct: 423 IRRAHRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYVGM 482


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: 595
Number of extensions: 41
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: 489
Length adjustment: 34
Effective length of query: 446
Effective length of database: 455
Effective search space:   202930
Effective search space used:   202930
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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