Alignments for a candidate for iolC in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Klebsiella michiganensis M5al

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate BWI76_RS03085 BWI76_RS03085 5-dehydro-2-deoxygluconokinase

Query= reanno::Koxy:BWI76_RS03085
         (637 letters)



>FitnessBrowser__Koxy:BWI76_RS03085
          Length = 637

 Score = 1292 bits (3344), Expect = 0.0
 Identities = 637/637 (100%), Positives = 637/637 (100%)

Query: 1   MNAAVKRLDVICIGRVAVDLYAQQIGARLEDVASFSKYLGGSSGNVAFGTAIQGLKSAML 60
           MNAAVKRLDVICIGRVAVDLYAQQIGARLEDVASFSKYLGGSSGNVAFGTAIQGLKSAML
Sbjct: 1   MNAAVKRLDVICIGRVAVDLYAQQIGARLEDVASFSKYLGGSSGNVAFGTAIQGLKSAML 60

Query: 61  ARVGDEHNGRFLRETLSRAGVDTEYLITDKQRLTALVMLGIKDQETFPLIFYRDNCADMA 120
           ARVGDEHNGRFLRETLSRAGVDTEYLITDKQRLTALVMLGIKDQETFPLIFYRDNCADMA
Sbjct: 61  ARVGDEHNGRFLRETLSRAGVDTEYLITDKQRLTALVMLGIKDQETFPLIFYRDNCADMA 120

Query: 121 LSPEDIKEEYIASSRALAVTGTHLSHANTREAVLKALEYARRHGLRTALDIDYRPVLWGL 180
           LSPEDIKEEYIASSRALAVTGTHLSHANTREAVLKALEYARRHGLRTALDIDYRPVLWGL
Sbjct: 121 LSPEDIKEEYIASSRALAVTGTHLSHANTREAVLKALEYARRHGLRTALDIDYRPVLWGL 180

Query: 181 TSLGDGETRFIESGQVTSQLQEVLHLFDLVVGTEEEFHIAGGSTDTLTALKNVRNATKAT 240
           TSLGDGETRFIESGQVTSQLQEVLHLFDLVVGTEEEFHIAGGSTDTLTALKNVRNATKAT
Sbjct: 181 TSLGDGETRFIESGQVTSQLQEVLHLFDLVVGTEEEFHIAGGSTDTLTALKNVRNATKAT 240

Query: 241 LVCKRGPMGCVVLEGAIPDNWDSVPLQQGVRVDVLNVLGAGDAFMSGLLRGWLNDEGWEQ 300
           LVCKRGPMGCVVLEGAIPDNWDSVPLQQGVRVDVLNVLGAGDAFMSGLLRGWLNDEGWEQ
Sbjct: 241 LVCKRGPMGCVVLEGAIPDNWDSVPLQQGVRVDVLNVLGAGDAFMSGLLRGWLNDEGWEQ 300

Query: 301 ACRYANACGALVVSRHGCAPAMPTKAELDDYLSRAESVPRPDIDDRLNHLHRVTSRRQAW 360
           ACRYANACGALVVSRHGCAPAMPTKAELDDYLSRAESVPRPDIDDRLNHLHRVTSRRQAW
Sbjct: 301 ACRYANACGALVVSRHGCAPAMPTKAELDDYLSRAESVPRPDIDDRLNHLHRVTSRRQAW 360

Query: 361 PELCIFAFDHRKQLADLALETGRDESCIPQLKLLLLAAAEAAADEAGLDGRSGILADGTY 420
           PELCIFAFDHRKQLADLALETGRDESCIPQLKLLLLAAAEAAADEAGLDGRSGILADGTY
Sbjct: 361 PELCIFAFDHRKQLADLALETGRDESCIPQLKLLLLAAAEAAADEAGLDGRSGILADGTY 420

Query: 421 GQRSLNAITGKGWWIGRPIEMPSSRPLRLEHGNIGSQLIDWPLEHVVKCLVFYHPADPAE 480
           GQRSLNAITGKGWWIGRPIEMPSSRPLRLEHGNIGSQLIDWPLEHVVKCLVFYHPADPAE
Sbjct: 421 GQRSLNAITGKGWWIGRPIEMPSSRPLRLEHGNIGSQLIDWPLEHVVKCLVFYHPADPAE 480

Query: 481 LRAEQDALLLEVWQACNKSGHELLLEIILPENGPDKDERHYHDMLEHFYQLGIQPDWWKL 540
           LRAEQDALLLEVWQACNKSGHELLLEIILPENGPDKDERHYHDMLEHFYQLGIQPDWWKL
Sbjct: 481 LRAEQDALLLEVWQACNKSGHELLLEIILPENGPDKDERHYHDMLEHFYQLGIQPDWWKL 540

Query: 541 PPLSSAEWERIGKLIAREDSWCRGILILGLDAPSDRLRAGFAEAAKHPMIKGFAVGRTIF 600
           PPLSSAEWERIGKLIAREDSWCRGILILGLDAPSDRLRAGFAEAAKHPMIKGFAVGRTIF
Sbjct: 541 PPLSSAEWERIGKLIAREDSWCRGILILGLDAPSDRLRAGFAEAAKHPMIKGFAVGRTIF 600

Query: 601 GQPSRRWMQGELSDEALINEVKRNYLTLIGYWREARG 637
           GQPSRRWMQGELSDEALINEVKRNYLTLIGYWREARG
Sbjct: 601 GQPSRRWMQGELSDEALINEVKRNYLTLIGYWREARG 637


Lambda     K      H
   0.320    0.137    0.422 

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: 1444
Number of extensions: 38
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: 637
Length of database: 637
Length adjustment: 38
Effective length of query: 599
Effective length of database: 599
Effective search space:   358801
Effective search space used:   358801
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: 54 (25.4 bits)

Align candidate BWI76_RS03085 BWI76_RS03085 (5-dehydro-2-deoxygluconokinase)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))

# 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/TIGR04382.hmm
# target sequence database:        /tmp/gapView.22547.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04382  [M=309]
Accession:   TIGR04382
Description: myo_inos_iolC_N: 5-dehydro-2-deoxygluconokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   3.1e-129  416.6   0.0     5e-129  415.9   0.0    1.3  1  lcl|FitnessBrowser__Koxy:BWI76_RS03085  BWI76_RS03085 5-dehydro-2-deoxyg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS03085  BWI76_RS03085 5-dehydro-2-deoxygluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.9   0.0    5e-129    5e-129       2     309 .]       8     332 ..       7     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.9 bits;  conditional E-value: 5e-129
                               TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreeler 72 
                                             ld+i+iGRv+vDlyaqqiga+ledv sf+kylGGs+ N+a+g+a  Glk+a++++vgd++ Grf+re+l+r
  lcl|FitnessBrowser__Koxy:BWI76_RS03085   8 LDVICIGRVAVDLYAQQIGARLEDVASFSKYLGGSSGNVAFGTAIQGLKSAMLARVGDEHNGRFLRETLSR 78 
                                             8********************************************************************** PP

                               TIGR04382  73 egvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskeps 143
                                              gvdt+ ++tdk+++t+lv+l+ikd+++fpl+fYR+n+aD+al+++d++ee+ia+++al+v+gt+ls+ ++
  lcl|FitnessBrowser__Koxy:BWI76_RS03085  79 AGVDTEYLITDKQRLTALVMLGIKDQETFPLIFYRDNCADMALSPEDIKEEYIASSRALAVTGTHLSHANT 149
                                             *********************************************************************** PP

                               TIGR04382 144 reavlkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEfeia 202
                                             reavlkale+a+++g +++lDiDYRpvlW+            ++ +++ +lq+vl+++d+++GteeEf+ia
  lcl|FitnessBrowser__Koxy:BWI76_RS03085 150 REAVLKALEYARRHGLRTALDIDYRPVLWGltslgdgetrfiESGQVTSQLQEVLHLFDLVVGTEEEFHIA 220
                                             *********************************************************************** PP

                               TIGR04382 203 agekddeaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasgllyg 268
                                              g++d+ +a+k++++++++++v+KrG+ G++v++++     ++    +g++v+vl+vlGaGDaF+sgll+g
  lcl|FitnessBrowser__Koxy:BWI76_RS03085 221 GGSTDTLTALKNVRNATKATLVCKRGPMGCVVLEGAipdnwDSVPLQQGVRVDVLNVLGAGDAFMSGLLRG 291
                                             ***********************************9999988888899*********************** PP

                               TIGR04382 269 llegedlekalelanAagaivvsrlscaeamptleeleefl 309
                                             +l++e +e+a+++anA+ga+vvsr++ca+ampt++el+++l
  lcl|FitnessBrowser__Koxy:BWI76_RS03085 292 WLNDEGWEQACRYANACGALVVSRHGCAPAMPTKAELDDYL 332
                                             *************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (637 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.84
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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