GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Shewanella sp. ANA-3

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 7024359 Shewana3_1551 phosphate acetyltransferase (RefSeq)

Query= BRENDA::Q8ZND6
         (714 letters)



>FitnessBrowser__ANA3:7024359
          Length = 717

 Score =  956 bits (2471), Expect = 0.0
 Identities = 480/715 (67%), Positives = 589/715 (82%), Gaps = 8/715 (1%)

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

Query: 61  STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120
            T+   EP  M+H E+L+ ++Q DVLME+IIA       + E ++VEGLVPTR H FA  
Sbjct: 61  PTVNPLEPFDMAHAEALIRADQTDVLMEQIIARAAECASNTETLIVEGLVPTRNHPFADD 120

Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180
           +NY IAK ++A+++F+ + G+DTP  L  R+E+  +S+GG  N  + G +INK+ APVD+
Sbjct: 121 VNYAIAKAMDADVIFIATPGSDTPTGLMNRLEIAYNSWGGKNNKRLIGAVINKIGAPVDD 180

Query: 181 QGRTRPDLSEIFDDS----SKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMAR 236
           +GR RPDLSE+FD      S A ++   P K    SPL +LG+VP++ DL+A RA D+A+
Sbjct: 181 EGRARPDLSEVFDHQGVQRSDASIMFQMPGK----SPLRILGSVPYNLDLVAPRASDLAK 236

Query: 237 HLNATIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNG 296
           HL A I+N G++ TRR++ VTFCARS+P+M+ H +  SLLVTS DR DV+V+ACLAAMNG
Sbjct: 237 HLRARILNAGEMNTRRLRKVTFCARSLPNMVNHIKTDSLLVTSGDRSDVIVSACLAAMNG 296

Query: 297 VEIGALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHER 356
           V+IGALLLTG YE +  I KLCE+AF TGLPVF+++TNTWQTSL++Q F+ EVPVDD  R
Sbjct: 297 VKIGALLLTGSYEPEPEILKLCEQAFETGLPVFLIDTNTWQTSLNIQRFDHEVPVDDAVR 356

Query: 357 IEKVQEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRT 416
           I+ VQEYVA++++  WIES+T  S R  RLSPPAFRY+LTELAR A K VVLPEGDEPRT
Sbjct: 357 IDLVQEYVASHIDQSWIESVTKNSPREHRLSPPAFRYKLTELARAAHKTVVLPEGDEPRT 416

Query: 417 VKAAAICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRK 476
           +KAAAICAERGIA CVLLG  DEI R+AA Q V LG G+ IVDP+ VR+ YV  +++LR+
Sbjct: 417 IKAAAICAERGIARCVLLGKKDEIQRIAAQQDVVLGEGVVIVDPDEVRDRYVEPMLDLRR 476

Query: 477 SKGMTEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLV 536
           +KG+TE VA+EQLEDN+VLGT+ML Q+EVDG+VSGAV+TTANTIRPPLQLIKTAPGSSLV
Sbjct: 477 NKGLTEVVAKEQLEDNMVLGTMMLAQNEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLV 536

Query: 537 SSVFFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSG 596
           SS+FFML+P+QV VYGDCAINPDP AEQLA+IAIQSA+SA AFGIEPRVAM+SYSTG SG
Sbjct: 537 SSIFFMLMPDQVLVYGDCAINPDPNAEQLADIAIQSAESAKAFGIEPRVAMISYSTGNSG 596

Query: 597 AGSDVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDL 656
            GSDV+KVREATR+A+EKRPDL+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVF+FPDL
Sbjct: 597 TGSDVDKVREATRIAKEKRPDLVIDGPLQYDAAVMPNVARSKAPNSPVAGQATVFVFPDL 656

Query: 657 NTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711
           NTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ
Sbjct: 657 NTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711


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: 1388
Number of extensions: 46
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: 717
Length adjustment: 39
Effective length of query: 675
Effective length of database: 678
Effective search space:   457650
Effective search space used:   457650
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 7024359 Shewana3_1551 (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.26053.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.8e-138  444.7   0.2   1.4e-137  444.2   0.2    1.2  1  lcl|FitnessBrowser__ANA3:7024359  Shewana3_1551 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024359  Shewana3_1551 phosphate acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.2   0.2  1.4e-137  1.4e-137       1     304 []     406     706 ..     406     706 .. 0.96

  Alignments for each domain:
  == domain 1  score: 444.2 bits;  conditional E-value: 1.4e-137
                         TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhkG 76 
                                       +vlPEg+e+r++kAaa++ae++ia++vll++k+e+++  + ++v l  g vv++dpd    +++yve + ++r++kG
  lcl|FitnessBrowser__ANA3:7024359 406 VVLPEGDEPRTIKAAAICAERGIARCVLLGKKDEIQRIaAQQDVVLGEG-VVIVDPDEV--RDRYVEPMLDLRRNKG 479
                                       69*********************************99733444555444.555666655..6*************** PP

                         TIGR00651  77 vtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCav 153
                                       +te  a+eql+D+++l++++++++e+dg+vsGav+tta+t+rp+lq+ikt++g++lvss+f+m  +++vlv++DCa+
  lcl|FitnessBrowser__ANA3:7024359 480 LTEVVAKEQLEDNMVLGTMMLAQNEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIFFMLMPDQVLVYGDCAI 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__ANA3:7024359 557 NPDPNAEQLADIAIQSAESAKAFG-IEPRVAMISYSTGNSGTGSDVDKVREATRIAKEKRPDLVIDGPLQYDAAVMP 632
                                       ************************.**************************************************** PP

                         TIGR00651 231 kvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                       +va++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa+v+div+++++ta
  lcl|FitnessBrowser__ANA3:7024359 633 NVARSKAPNSPVAGQATVFVFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTA 706
                                       ************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (717 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: 20.24
//
[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