GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Herbaspirillum seropedicae SmR1

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate HSERO_RS22235 HSERO_RS22235 short-chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>FitnessBrowser__HerbieS:HSERO_RS22235
          Length = 690

 Score =  972 bits (2512), Expect = 0.0
 Identities = 467/690 (67%), Positives = 565/690 (81%)

Query: 10  LANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWV 69
           +A+ WD+  AA + EP+ LLYRSNLLG+DK ITN+GGGNTSAK+   DPLTG+ VEVLWV
Sbjct: 1   IASAWDEAYAATLDEPQLLLYRSNLLGADKEITNFGGGNTSAKIAMPDPLTGQTVEVLWV 60

Query: 70  KGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTP 129
           KGSGGD+G+IK+DGF+TLYMDKL AL+  YRG+E EDEMVGYLPHCT+NLN RAASIDTP
Sbjct: 61  KGSGGDLGSIKLDGFATLYMDKLEALRSRYRGLEHEDEMVGYLPHCTYNLNARAASIDTP 120

Query: 130 LHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQ 189
           LHAY+P+ HVDHMHPDA+IAIAA KNSR+LT++IF  E+GWLPW+RPGY+LGL LE+  +
Sbjct: 121 LHAYIPRRHVDHMHPDAVIAIAACKNSRDLTARIFEGELGWLPWQRPGYDLGLKLEQLVR 180

Query: 190 ENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPAFGGRSKPVLAAA 249
             P  +G+VLE HGLFTWGD+A+E YE T+ +I RA AW    +  PAFGG     L  A
Sbjct: 181 AQPHLKGIVLEGHGLFTWGDSARECYENTLNVIRRADAWLAANSRTPAFGGARYQALPKA 240

Query: 250 DRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTK 309
           +RAA+A ++MP++RG IS GE K+GHFDDSQAVLDFV S  L  LAALGTSCPDHFLRTK
Sbjct: 241 ERAALAARIMPLLRGKISKGEYKLGHFDDSQAVLDFVCSNDLAALAALGTSCPDHFLRTK 300

Query: 310 IRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPG 369
           IRPLV+DF P QPD+    A L  A+  YR DYAAYY+RC R +SPAMRDPN V+YL+PG
Sbjct: 301 IRPLVLDFSPQQPDLAALEASLDAALEAYRQDYAAYYQRCARPNSPAMRDPNPVIYLIPG 360

Query: 370 VGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRM 429
           VGM++FAKDKATARI+ EFY+NA+NVMRGA+GV +YVGLPEQEAFDIEYWLLEEAKLQRM
Sbjct: 361 VGMLSFAKDKATARIAGEFYINAVNVMRGANGVDSYVGLPEQEAFDIEYWLLEEAKLQRM 420

Query: 430 PKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDF 489
           PKPKSLAGRIALVTGG GGIG+A A +L+ EGACV+L DID++AL++AQ  L    G D 
Sbjct: 421 PKPKSLAGRIALVTGGGGGIGQAVARQLLAEGACVMLTDIDQSALDSAQQSLLKHGGPDA 480

Query: 490 VRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILAT 549
           +  V  ++TSEA V +      L FGG+D+LVSNAG+A+++ ++DT+L +W +N+ +LAT
Sbjct: 481 IGVVRADITSEADVTTILNSVALRFGGIDLLVSNAGIASASPLQDTSLEVWQRNLSVLAT 540

Query: 550 GYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGAS 609
           GYFLVSR AF     Q  GG++V+VASKNGL AS GASAYCTAKAAEIHLARC+ALEGA 
Sbjct: 541 GYFLVSRAAFSSMLTQGLGGSIVYVASKNGLVASAGASAYCTAKAAEIHLARCIALEGAP 600

Query: 610 AQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIAE 669
             IRVNVVNPDAV+RGS+IW G+WKE+RAA+ K++ D++E  YR+RSMLK SV PEDIAE
Sbjct: 601 HGIRVNVVNPDAVIRGSRIWDGKWKEERAASNKIEADDVEEFYRQRSMLKRSVLPEDIAE 660

Query: 670 AIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699
           A+YF AS+ SAKSTGNI+NVDAGNA +FTR
Sbjct: 661 AVYFFASEKSAKSTGNILNVDAGNAGAFTR 690


Lambda     K      H
   0.317    0.133    0.393 

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: 1303
Number of extensions: 36
Number of successful extensions: 1
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: 699
Length of database: 690
Length adjustment: 39
Effective length of query: 660
Effective length of database: 651
Effective search space:   429660
Effective search space used:   429660
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: 54 (25.4 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