Alignments for a candidate for fucO in Klebsiella michiganensis M5al

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.3210339.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  FitnessBrowser__Koxy:BWI76_RS22480  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Koxy:BWI76_RS22480  
   #    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 nrlilnevsyfGaGaiedivkevkrrgfkkalvvtdkdliklgvvdkvlelldeaklayelfdevvpnPtvevvk 76 
                                         +r+ilne+syfG G+i+ iv+evk+rgfkkalvvtdkdli+++v++kvl++ld a l+y +fd+vvpnPt+evv+
  FitnessBrowser__Koxy:BWI76_RS22480   3 YRMILNETSYFGPGSISCIVDEVKKRGFKKALVVTDKDLIRFNVATKVLAILDGAGLPYSIFDDVVPNPTIEVVQ 77 
                                         79************************************************************************* PP

                           TIGR02638  77 eGlaafkesgadyliaiGGGspidtakaigiivnnPefadvvsleGvadtkkkavpiiaipttaGtaaevtinyv 151
                                         +G+++fk+sgadyliaiGGGsp+dt+kaigii+nnPefadv+sleG adtk++avp+iaipttaGtaaevtinyv
  FitnessBrowser__Koxy:BWI76_RS22480  78 QGVETFKQSGADYLIAIGGGSPQDTCKAIGIIINNPEFADVRSLEGGADTKNAAVPMIAIPTTAGTAAEVTINYV 152
                                         *************************************************************************** PP

                           TIGR02638 152 itdeekkrklvivdpkdiPavavvdaelmlslPksltaatGldalthaiegyitkgaweltdalelkaieliara 226
                                         itd +++rk+v+ dp+diP va++dae+m+s+P+sl+aatG+dalthaiegyitkgaweltd+l+lkaie+i+r+
  FitnessBrowser__Koxy:BWI76_RS22480 153 ITDVQNRRKFVCYDPHDIPLVAIIDAEMMASMPASLKAATGVDALTHAIEGYITKGAWELTDMLHLKAIEVIGRS 227
                                         *************************************************************************** PP

                           TIGR02638 227 lksavedgkdkeareelalgqyvaGmafsnvGlGlvhglahplgalydlPhGvanaillPivmefnaekagekyr 301
                                         l+++v++  d+++ e +algqy+aGm+fsnvGlGlvhg+ahplga+y +PhGvana+llP++m++nae++gekyr
  FitnessBrowser__Koxy:BWI76_RS22480 228 LRASVQG--DAQGAEGMALGQYIAGMGFSNVGLGLVHGMAHPLGAFYGTPHGVANAVLLPHIMAYNAEYTGEKYR 300
                                         *******..****************************************************************** PP

                           TIGR02638 302 eiakamgvk.teelseeeareaaveavktlskrvgiPeklselgvkeediealaeaaladvCtggnPreataeei 375
                                         +ia a+g k ++ +  +ear+aa+eav +l+++v+iP++l+++g+keedi+ala aaladvCtggnPr+++ eei
  FitnessBrowser__Koxy:BWI76_RS22480 301 DIAVALGNKsAATMPIAEARQAAIEAVAQLNRDVNIPARLRDVGMKEEDIDALAAAALADVCTGGNPRDTNLEEI 375
                                         *********8899************************************************************** PP

                           TIGR02638 376 eely 379
                                         ++ly
  FitnessBrowser__Koxy:BWI76_RS22480 376 KTLY 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.72
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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