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.1382.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.17
//
[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