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.10154.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: 14.08
//
[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:

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