Alignments for a candidate for aldA in Herbaspirillum seropedicae SmR1

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources