Alignments for a candidate for pta in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Klebsiella michiganensis M5al

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate BWI76_RS20240 BWI76_RS20240 phosphate acetyltransferase

Query= BRENDA::Q8ZND6
         (714 letters)



>FitnessBrowser__Koxy:BWI76_RS20240
          Length = 714

 Score = 1338 bits (3462), Expect = 0.0
 Identities = 689/713 (96%), Positives = 703/713 (98%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60
           MSR IMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTI+RAN
Sbjct: 1   MSRTIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIIRAN 60

Query: 61  STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120
           S LPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANT+DAEVVLVEGLVPTRKHQFAQS
Sbjct: 61  SDLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTQDAEVVLVEGLVPTRKHQFAQS 120

Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180
           LNYEIAKTLNAEIVFVMSQGTDTPEQL ERIELTRSSFGGAKNT+ITGVI+NKLNAPVDE
Sbjct: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLKERIELTRSSFGGAKNTSITGVIVNKLNAPVDE 180

Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240
           QGRTRPDLSEIFDDSSKA+V+KIDPA+LQ+ SPLPVLGAVPWSFDLIATRAIDMA HLNA
Sbjct: 181 QGRTRPDLSEIFDDSSKAKVVKIDPAQLQDGSPLPVLGAVPWSFDLIATRAIDMAHHLNA 240

Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300
           TIINEGDI TRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG
Sbjct: 241 TIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300

Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360
           A+LLTG YEMD R+SKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV
Sbjct: 301 AILLTGAYEMDPRVSKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360

Query: 361 QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA 420
           QEYVANY+NA+WIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEG+EPRTVKAA
Sbjct: 361 QEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGNEPRTVKAA 420

Query: 421 AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM 480
           AICAERGIATCVLLGNPDEI RVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM
Sbjct: 421 AICAERGIATCVLLGNPDEITRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM 480

Query: 481 TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540
           TE VAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF
Sbjct: 481 TEAVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540

Query: 541 FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD 600
           FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD
Sbjct: 541 FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD 600

Query: 601 VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN 660
           VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN
Sbjct: 601 VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN 660

Query: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQQ 713
           TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQ+SQQQ
Sbjct: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSSQQQ 713


Lambda     K      H
   0.316    0.131    0.364 

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: 1574
Number of extensions: 32
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: 714
Length of database: 714
Length adjustment: 39
Effective length of query: 675
Effective length of database: 675
Effective search space:   455625
Effective search space used:   455625
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 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate BWI76_RS20240 BWI76_RS20240 (phosphate acetyltransferase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))

# 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/TIGR00651.hmm
# target sequence database:        /tmp/gapView.32045.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00651  [M=304]
Accession:   TIGR00651
Description: pta: phosphate acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.8e-141  457.0   0.1   2.9e-141  456.3   0.1    1.3  1  lcl|FitnessBrowser__Koxy:BWI76_RS20240  BWI76_RS20240 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS20240  BWI76_RS20240 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.3   0.1  2.9e-141  2.9e-141       1     304 []     406     706 ..     406     706 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.3 bits;  conditional E-value: 2.9e-141
                               TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlye 70 
                                             +vlPEg+e+r++kAaa++ae++ia++vll+n +e++++ ++++v+l +g  +v+ p+v   +e+yv rl+e
  lcl|FitnessBrowser__Koxy:BWI76_RS20240 406 VVLPEGNEPRTVKAAAICAERGIATCVLLGNPDEITRVaASQGVELGAGIEIVD-PEVV--RESYVARLVE 473
                                             69***********************************97789999998876655.5555..5********* PP

                               TIGR00651  71 krkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimek 141
                                             +rk kG+te+ areql+D+v+l++l++e++e+dglvsGav+tta+t+rp+lq+ikt++g++lvssvf+m +
  lcl|FitnessBrowser__Koxy:BWI76_RS20240 474 LRKSKGMTEAVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLL 544
                                             *********************************************************************** PP

                               TIGR00651 142 eeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkek 212
                                             +e+v+v++DCa+++dP+ae+LAeiA+qsa+sa ++g +ep+va+lsyst++sg+g++vekv+eA+++++ek
  lcl|FitnessBrowser__Koxy:BWI76_RS20240 545 PEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFG-IEPRVAMLSYSTGTSGAGSDVEKVREATRLAQEK 614
                                             ************************************.********************************** PP

                               TIGR00651 213 epdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakP 283
                                             +pdl++dG+lq+DaA++++va++kap+s+vag+a+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kP
  lcl|FitnessBrowser__Koxy:BWI76_RS20240 615 RPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKP 685
                                             *********************************************************************** PP

                               TIGR00651 284 vnDLsRGasvedivnvviita 304
                                             vnDLsRGa+v+div+++++ta
  lcl|FitnessBrowser__Koxy:BWI76_RS20240 686 VNDLSRGALVDDIVYTIALTA 706
                                             *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (714 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: 00:00:00.01
# Mc/sec: 17.14
//
[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