Alignments for a candidate for pta in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Shewanella amazonensis SB2B

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 6937324 Sama_1494 phosphate acetyltransferase (RefSeq)

Query= BRENDA::Q8ZND6
         (714 letters)



>FitnessBrowser__SB2B:6937324
          Length = 712

 Score =  964 bits (2493), Expect = 0.0
 Identities = 480/712 (67%), Positives = 587/712 (82%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60
           MSR IML+P GT VGLTS+SLG++RA+ER GV++  FKPI+Q R     P+++TTI+  +
Sbjct: 1   MSRNIMLVPIGTGVGLTSLSLGMVRALERHGVKVQFFKPISQQRPADSGPERSTTILSKS 60

Query: 61  STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120
            T+   EP  M H ESL+ ++Q DVLME+IIA       + E +++EGLVPTR H F+  
Sbjct: 61  PTVNPLEPFDMQHAESLIRTDQTDVLMEQIIARASEIAANTETLIIEGLVPTRSHSFSDD 120

Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180
           +NY IAK L+A+++F+ + G DTP  L  R+E+  +S+GGAKN  + G +INK+ APVD+
Sbjct: 121 VNYAIAKALDADVIFIATPGNDTPNALMNRLEIAYNSWGGAKNKRLIGAVINKIGAPVDD 180

Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240
           +GRTRPDLSE+FD     +       +L   S L +LG+VP++ DL++ RA D+A+HL+A
Sbjct: 181 EGRTRPDLSEVFDHQDIQKGDATAMFQLPGKSKLRILGSVPYNLDLVSPRASDLAKHLHA 240

Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300
            I+N G++ TRR++ VTFCARSIP+ML HFR  SLLVTS DR DV+VAACLAAMNGV+IG
Sbjct: 241 RILNAGEMNTRRLRKVTFCARSIPNMLSHFRTDSLLVTSGDRSDVIVAACLAAMNGVKIG 300

Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360
           ALLLTG YE +  + KLCE+AF TGLPVFM++TNTWQTSL++Q FN EVPVDD  RIE V
Sbjct: 301 ALLLTGSYEPEPEVLKLCEQAFETGLPVFMIDTNTWQTSLNIQRFNHEVPVDDAVRIELV 360

Query: 361 QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA 420
           QEYVA++++  WIES+T  S R  RLSPPAFRY+LTELAR A K +VLPEGDEPRT+KAA
Sbjct: 361 QEYVASHIDQSWIESVTENSPREHRLSPPAFRYKLTELARAAKKCIVLPEGDEPRTIKAA 420

Query: 421 AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM 480
           +ICAERGIA CVLLG  D+I R+AA+Q V LG G+EI+DPE +RE YV  ++ LR+ KG+
Sbjct: 421 SICAERGIARCVLLGKKDDILRIAAAQDVVLGEGVEILDPEDIREQYVEPMLNLRRHKGL 480

Query: 481 TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540
           TE VAREQLEDN+VL T+ML +DEVDG+VSGAV+TTANTIRPPLQLIKTAPGSSLVSS+F
Sbjct: 481 TEVVAREQLEDNMVLATMMLAEDEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIF 540

Query: 541 FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD 600
           FML+P+QV VYGDCAINPDP AEQLA+IAIQSA+SA AFGIEPRVAM+SYSTG SG GSD
Sbjct: 541 FMLMPDQVLVYGDCAINPDPNAEQLADIAIQSAESAKAFGIEPRVAMISYSTGNSGTGSD 600

Query: 601 VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN 660
           V+KVREATR+A+EKRPDL+IDGPLQYDAAVM +VA+SKAP+SPVAG+ATVF+FPDLNTGN
Sbjct: 601 VDKVREATRIAKEKRPDLVIDGPLQYDAAVMPNVARSKAPDSPVAGKATVFVFPDLNTGN 660

Query: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQ 712
           TTYKAVQRSA+LISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQA+QQ
Sbjct: 661 TTYKAVQRSAELISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQATQQ 712


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: 1361
Number of extensions: 41
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: 714
Length of database: 712
Length adjustment: 39
Effective length of query: 675
Effective length of database: 673
Effective search space:   454275
Effective search space used:   454275
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 6937324 Sama_1494 (phosphate acetyltransferase (RefSeq))
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.10255.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.1e-137  443.0   0.1   4.4e-137  442.5   0.1    1.2  1  lcl|FitnessBrowser__SB2B:6937324  Sama_1494 phosphate acetyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937324  Sama_1494 phosphate acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.5   0.1  4.4e-137  4.4e-137       1     304 []     406     706 ..     406     706 .. 0.97

  Alignments for each domain:
  == domain 1  score: 442.5 bits;  conditional E-value: 4.4e-137
                         TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhkG 76 
                                       ivlPEg+e+r++kAa+++ae++ia++vll++k+++ +  +a++v l  g  +++++d++   e+yve + ++r+hkG
  lcl|FitnessBrowser__SB2B:6937324 406 IVLPEGDEPRTIKAASICAERGIARCVLLGKKDDILRIaAAQDVVLGEGVEILDPEDIR---EQYVEPMLNLRRHKG 479
                                       8***********************************98667777777776666666666...*************** PP

                         TIGR00651  77 vtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCav 153
                                       +te  areql+D+++la+++++ +e+dg+vsGav+tta+t+rp+lq+ikt++g++lvss+f+m  +++vlv++DCa+
  lcl|FitnessBrowser__SB2B:6937324 480 LTEVVAREQLEDNMVLATMMLAEDEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIFFMLMPDQVLVYGDCAI 556
                                       ***************************************************************************** PP

                         TIGR00651 154 avdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlve 230
                                       ++dPnae+LA+iA+qsa+sak++g +ep+va++syst+ sg g++v+kv+eA++i+kek+pdl++dG+lq+DaA+++
  lcl|FitnessBrowser__SB2B:6937324 557 NPDPNAEQLADIAIQSAESAKAFG-IEPRVAMISYSTGNSGTGSDVDKVREATRIAKEKRPDLVIDGPLQYDAAVMP 632
                                       ************************.**************************************************** PP

                         TIGR00651 231 kvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                       +va++kap+s+vagka+vfvFPdL++Gn++Yk+vqR+a++ +iGP+lqG++kPvnDLsRGa+v+div+++++ta
  lcl|FitnessBrowser__SB2B:6937324 633 NVARSKAPDSPVAGKATVFVFPDLNTGNTTYKAVQRSAELISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTA 706
                                       ************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (712 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.06
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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