GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Klebsiella michiganensis M5al

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate BWI76_RS22480 BWI76_RS22480 lactaldehyde reductase

Query= SwissProt::P0A9S1
         (382 letters)



>FitnessBrowser__Koxy:BWI76_RS22480
          Length = 383

 Score =  536 bits (1380), Expect = e-157
 Identities = 267/379 (70%), Positives = 310/379 (81%), Gaps = 1/379 (0%)

Query: 1   MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLA 60
           MA RMILNET++FG G++  + DEVK+RG++KAL+VTDK L++  V  KV   +D AGL 
Sbjct: 1   MAYRMILNETSYFGPGSISCIVDEVKKRGFKKALVVTDKDLIRFNVATKVLAILDGAGLP 60

Query: 61  WAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRS 120
           ++I+D VVPNPTI VV++G+  F+ SGADYLIAIGGGSPQDTCKAIGII NNPEFADVRS
Sbjct: 61  YSIFDDVVPNPTIEVVQQGVETFKQSGADYLIAIGGGSPQDTCKAIGIIINNPEFADVRS 120

Query: 121 LEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADM 180
           LEG + T   +VP++AIPTTAGTAAEVTINYVITD + RRKFVC DPHDIP VA IDA+M
Sbjct: 121 LEGGADTKNAAVPMIAIPTTAGTAAEVTINYVITDVQNRRKFVCYDPHDIPLVAIIDAEM 180

Query: 181 MDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGE 240
           M  MP +LKAATGVDALTHAIEGYIT+GAW LTD LH+KAIE+I  +LR SV GD    E
Sbjct: 181 MASMPASLKAATGVDALTHAIEGYITKGAWELTDMLHLKAIEVIGRSLRASVQGDAQGAE 240

Query: 241 EMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYR 300
            MALGQY+AGMGFSNVGLGLVHGMAHPLGAFY TPHGVANA+LLPH+M YNA++TGEKYR
Sbjct: 241 GMALGQYIAGMGFSNVGLGLVHGMAHPLGAFYGTPHGVANAVLLPHIMAYNAEYTGEKYR 300

Query: 301 DIARVMGVK-VEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDD 359
           DIA  +G K    M + EAR AA+EAV  LNRDV IP  LRDVG+++EDI ALA AAL D
Sbjct: 301 DIAVALGNKSAATMPIAEARQAAIEAVAQLNRDVNIPARLRDVGMKEEDIDALAAAALAD 360

Query: 360 VCTGGNPREATLEDIVELY 378
           VCTGGNPR+  LE+I  LY
Sbjct: 361 VCTGGNPRDTNLEEIKTLY 379


Lambda     K      H
   0.319    0.136    0.404 

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: 570
Number of extensions: 22
Number of successful extensions: 2
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: 382
Length of database: 383
Length adjustment: 30
Effective length of query: 352
Effective length of database: 353
Effective search space:   124256
Effective search space used:   124256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS22480 BWI76_RS22480 (lactaldehyde reductase)
to HMM TIGR02638 (fucO: lactaldehyde reductase (EC 1.1.1.77))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02638.hmm
# target sequence database:        /tmp/gapView.32447.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02638  [M=379]
Accession:   TIGR02638
Description: lactal_redase: lactaldehyde reductase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.5e-196  636.3   5.5   8.5e-196  636.1   5.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS22480  BWI76_RS22480 lactaldehyde reduc


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS22480  BWI76_RS22480 lactaldehyde reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  636.1   5.5  8.5e-196  8.5e-196       2     379 .]       3     379 ..       2     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 636.1 bits;  conditional E-value: 8.5e-196
                               TIGR02638   2 nrlilnevsyfGaGaiedivkevkrrgfkkalvvtdkdliklgvvdkvlelldeaklayelfdevvpnPtv 72 
                                             +r+ilne+syfG G+i+ iv+evk+rgfkkalvvtdkdli+++v++kvl++ld a l+y +fd+vvpnPt+
  lcl|FitnessBrowser__Koxy:BWI76_RS22480   3 YRMILNETSYFGPGSISCIVDEVKKRGFKKALVVTDKDLIRFNVATKVLAILDGAGLPYSIFDDVVPNPTI 73 
                                             79********************************************************************* PP

                               TIGR02638  73 evvkeGlaafkesgadyliaiGGGspidtakaigiivnnPefadvvsleGvadtkkkavpiiaipttaGta 143
                                             evv++G+++fk+sgadyliaiGGGsp+dt+kaigii+nnPefadv+sleG adtk++avp+iaipttaGta
  lcl|FitnessBrowser__Koxy:BWI76_RS22480  74 EVVQQGVETFKQSGADYLIAIGGGSPQDTCKAIGIIINNPEFADVRSLEGGADTKNAAVPMIAIPTTAGTA 144
                                             *********************************************************************** PP

                               TIGR02638 144 aevtinyvitdeekkrklvivdpkdiPavavvdaelmlslPksltaatGldalthaiegyitkgaweltda 214
                                             aevtinyvitd +++rk+v+ dp+diP va++dae+m+s+P+sl+aatG+dalthaiegyitkgaweltd+
  lcl|FitnessBrowser__Koxy:BWI76_RS22480 145 AEVTINYVITDVQNRRKFVCYDPHDIPLVAIIDAEMMASMPASLKAATGVDALTHAIEGYITKGAWELTDM 215
                                             *********************************************************************** PP

                               TIGR02638 215 lelkaieliaralksavedgkdkeareelalgqyvaGmafsnvGlGlvhglahplgalydlPhGvanaill 285
                                             l+lkaie+i+r+l+++v++  d+++ e +algqy+aGm+fsnvGlGlvhg+ahplga+y +PhGvana+ll
  lcl|FitnessBrowser__Koxy:BWI76_RS22480 216 LHLKAIEVIGRSLRASVQG--DAQGAEGMALGQYIAGMGFSNVGLGLVHGMAHPLGAFYGTPHGVANAVLL 284
                                             *******************..************************************************** PP

                               TIGR02638 286 Pivmefnaekagekyreiakamgvk.teelseeeareaaveavktlskrvgiPeklselgvkeediealae 355
                                             P++m++nae++gekyr+ia a+g k ++ +  +ear+aa+eav +l+++v+iP++l+++g+keedi+ala 
  lcl|FitnessBrowser__Koxy:BWI76_RS22480 285 PHIMAYNAEYTGEKYRDIAVALGNKsAATMPIAEARQAAIEAVAQLNRDVNIPARLRDVGMKEEDIDALAA 355
                                             *************************8899****************************************** PP

                               TIGR02638 356 aaladvCtggnPreataeeieely 379
                                             aaladvCtggnPr+++ eei++ly
  lcl|FitnessBrowser__Koxy:BWI76_RS22480 356 AALADVCTGGNPRDTNLEEIKTLY 379
                                             **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (379 nodes)
Target sequences:                          1  (383 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.80
//
[ok]

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