Alignments for a candidate for uxuA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxuA in Klebsiella michiganensis M5al

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate BWI76_RS23640 BWI76_RS23640 mannonate dehydratase

Query= metacyc::MONOMER-17955
         (360 letters)



>FitnessBrowser__Koxy:BWI76_RS23640
          Length = 355

 Score =  461 bits (1187), Expect = e-134
 Identities = 212/356 (59%), Positives = 272/356 (76%), Gaps = 1/356 (0%)

Query: 1   MKLVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLK 60
           M++  RW+G + D + LE IRQ+PGVEGVVGAL+D+  GEVWP E+I  L E    AGLK
Sbjct: 1   MQMTMRWFGPQEDKIPLEYIRQVPGVEGVVGALYDVAPGEVWPVEKIKALIEQAHAAGLK 60

Query: 61  LEVIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKK 120
           +EVIESVN+H+DIK+G   RDRYI+NYK+TIRNLA  GVKV+CYNFMPVFDWM+TD++  
Sbjct: 61  MEVIESVNIHDDIKIGSAERDRYIDNYKQTIRNLAGFGVKVICYNFMPVFDWMKTDMNYV 120

Query: 121 LPDGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWDRLEKLRETFELYKNVDEE 180
           LPDGS TM ++ R I+    D ++K V E + GF LPGWE +RL K++E F  Y++VD+ 
Sbjct: 121 LPDGSLTMAFEKRGIDKSLED-VVKEVLENANGFALPGWEPERLAKVQELFARYRDVDDT 179

Query: 181 KLFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPYN 240
           +L ENL YFL  VIPVCEE  VK+AIHPDDPP+SIFGLPR++ N  ++  +   VDSP N
Sbjct: 180 RLRENLFYFLREVIPVCEEVGVKMAIHPDDPPYSIFGLPRVVKNHADLALICDTVDSPAN 239

Query: 241 GITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHDL 300
           GIT C GS+  +P+NN+ E++  F +  R+HFAHVRN+K   +K FYE+AHPS  GS D+
Sbjct: 240 GITLCTGSIAEDPDNNVYEILAEFTRRKRLHFAHVRNIKLIKDKDFYESAHPSAYGSLDM 299

Query: 301 FEVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDKMK 356
           + +M+A HD G++GYIRPDHGR IWGE  RPGYGLYDRALG TY++GLWEA++K K
Sbjct: 300 YRIMQALHDNGFDGYIRPDHGRFIWGETGRPGYGLYDRALGVTYLMGLWEALEKQK 355


Lambda     K      H
   0.322    0.142    0.448 

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: 493
Number of extensions: 21
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: 360
Length of database: 355
Length adjustment: 29
Effective length of query: 331
Effective length of database: 326
Effective search space:   107906
Effective search space used:   107906
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS23640 BWI76_RS23640 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# 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/TIGR00695.hmm
# target sequence database:        /tmp/gapView.27065.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.5e-125  403.8   0.0    7.3e-68  215.4   0.0    2.0  2  lcl|FitnessBrowser__Koxy:BWI76_RS23640  BWI76_RS23640 mannonate dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23640  BWI76_RS23640 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.1   3.2e-59   3.2e-59       1     134 [.       1     136 [.       1     151 [. 0.95
   2 !  215.4   0.0   7.3e-68   7.3e-68     180     389 ..     154     353 ..     137     355 .] 0.92

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 3.2e-59
                               TIGR00695   1 meqtfrwyGr.ndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvhe 69 
                                             m++t+rw+G+ +d + le++rq+ G++G+v al+++  Gevw ve+ik+  e+ + aGl+++v+esv++h+
  lcl|FitnessBrowser__Koxy:BWI76_RS23640   1 MQMTMRWFGPqEDKIPLEYIRQVpGVEGVVGALYDVAPGEVWPVEKIKALIEQAHAAGLKMEVIESVNIHD 71 
                                             89********99*********************************************************** PP

                               TIGR00695  70 eiklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikva 134
                                             +ik+++ e+++yi+nykqt+rnla++G+kv+cynfmpv+dw +td++y+l+dGs ++ f+k  ++
  lcl|FitnessBrowser__Koxy:BWI76_RS23640  72 DIKIGSAERDRYIDNYKQTIRNLAGFGVKVICYNFMPVFDWMKTDMNYVLPDGSLTMAFEKRGID 136
                                             ************************************************************97764 PP

  == domain 2  score: 215.4 bits;  conditional E-value: 7.3e-68
                               TIGR00695 180 glpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivst 250
                                             +lpG+e+ e+l++++el+++y+d+d+ +lrenl +fl+e++pv eevGvkmaihpddpp+ i+Glpr+v  
  lcl|FitnessBrowser__Koxy:BWI76_RS23640 154 ALPGWEP-ERLAKVQELFARYRDVDDTRLRENLFYFLREVIPVCEEVGVKMAIHPDDPPYSIFGLPRVVKN 223
                                             69*****.*************************************************************** PP

                               TIGR00695 251 iedmkklveisdspangitlctGsyGvradndlvelakqfa..driyfahlrsvkreenpktfheaahlek 319
                                              +d+  + +++dspangitlctGs+   +dn++ e+  +f+  +r++fah+r++k  ++  +f+e+ah + 
  lcl|FitnessBrowser__Koxy:BWI76_RS23640 224 HADLALICDTVDSPANGITLCTGSIAEDPDNNVYEILAEFTrrKRLHFAHVRNIKLIKDK-DFYESAHPSA 293
                                             ****************************************8334689********99887.*******987 PP

                               TIGR00695 320 dvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelalkk 389
                                              ++l   +  +++ +h +  +G    + +rpdhGr +++   +  +pGy++++r++G+++l Gl+ al+k
  lcl|FitnessBrowser__Koxy:BWI76_RS23640 294 YGSLD--MYRIMQALHDNGFDG----Y-IRPDHGRFIWG---ETGRPGYGLYDRALGVTYLMGLWEALEK 353
                                             76665..557888889999999....6.8**********...99************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (355 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 3.87
//
[ok]

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:

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
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