Alignments for a candidate for fadA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Herbaspirillum seropedicae SmR1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate HSERO_RS19990 HSERO_RS19990 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__HerbieS:HSERO_RS19990
          Length = 400

 Score =  570 bits (1469), Expect = e-167
 Identities = 289/401 (72%), Positives = 339/401 (84%), Gaps = 2/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M+DVFICDAIRTPIGR+GGAL  VRADDL AVPL+AL+E NP V W  VD+V +GCANQA
Sbjct: 1   MKDVFICDAIRTPIGRYGGALKDVRADDLGAVPLRALMERNPQVDWKAVDDVIYGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+LLLAGLP+ +PG T+NRLC SGMDA+GTA RAI SGE +L IAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQEVPGSTINRLCGSGMDALGTAARAIKSGETQLMIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +RAPFVMGKA+S +SR   ++DTTIGWRF+N LMK +YGVD+MPETA+NVA D++VSRAD
Sbjct: 121 TRAPFVMGKADSAFSRQAAIQDTTIGWRFVNALMKQKYGVDAMPETAENVAVDFKVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239
           QD FA+RSQ KAAAAQA G  A+EIVPV I  KKG+ I V +DEH R  T++EAL +LK 
Sbjct: 181 QDQFAVRSQAKAAAAQANGTLAQEIVPVVIPQKKGDPITVTQDEHPR-ATSMEALARLKG 239

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
           V  PD +VTAGNASGVNDGA AL+LASAEAV+K+ L PRAR+LGMA+ GVAPR+MG+GP 
Sbjct: 240 VVKPDGSVTAGNASGVNDGACALLLASAEAVEKYQLKPRARILGMATAGVAPRIMGMGPA 299

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PA +K+  +LG+ +   DVIELNEAFASQGLAVLRELGVADD  +VNPNGGAIALGHPLG
Sbjct: 300 PASKKVLAQLGMTIDQMDVIELNEAFASQGLAVLRELGVADDDARVNPNGGAIALGHPLG 359

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           MSGARLV TA +QLE++GGR  L TMC+GVGQG+A+ IERV
Sbjct: 360 MSGARLVTTATYQLERTGGRYALCTMCIGVGQGIAMVIERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 546
Number of extensions: 18
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate HSERO_RS19990 HSERO_RS19990 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.31006.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.8e-138  446.2   6.9   5.4e-138  446.0   6.9    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19990  HSERO_RS19990 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19990  HSERO_RS19990 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.0   6.9  5.4e-138  5.4e-138       1     385 []       6     398 ..       6     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 446.0 bits;  conditional E-value: 5.4e-138
                                  TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 
                                                i da+Rtpig++gg+lk+++a+dL+a  +++l+er+ ++d +++d+vi+G++ qage+  n+aR+ +l
  lcl|FitnessBrowser__HerbieS:HSERO_RS19990   6 ICDAIRTPIGRYGGALKDVRADDLGAVPLRALMERNpQVDWKAVDDVIYGCANQAGEDnRNVARMSLL 73 
                                                789*******99**********************************************9********* PP

                                  TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgka 134
                                                 aglp++vp+ t+nr+C+Sg++A+ +aa++ik+Ge ++++aGGvEsm+r+p+++ ++    s+  ++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS19990  74 LAGLPQEVPGSTINRLCGSGMDALGTAARAIKSGETQLMIAGGVESMTRAPFVMGKAD---SAFSRQA 138
                                                ****************************************************999973...3333344 PP

                                  TIGR01930 135 kledqllkdl..........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkde 192
                                                  +d+++  +          ++   +m etAen+a ++++sR +qD++a+rS+ kaa+A+++g +++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS19990 139 AIQDTTI--GwrfvnalmkqKYGVDAMPETAENVAVDFKVSRADQDQFAVRSQAKAAAAQANGTLAQE 204
                                                4444222..13356778887666679****************************************** PP

                                  TIGR01930 193 ivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseev 257
                                                ivpv++++k   + +v++De++r  t++e+La+Lk + k ++gs vtAgN+s++nDGA+alll+s e+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19990 205 IVPVVIPQKkgdPITVTQDEHPR-ATSMEALARLKGVVK-PDGS-VTAGNASGVNDGACALLLASAEA 269
                                                *******999*999*********.899***********9.69*7.*********************** PP

                                  TIGR01930 258 akelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelg 325
                                                +++++l+p ari ++a+agv p++mg+gp+pA++k+L++ g++i+++d++E+nEAFA+q lav +elg
  lcl|FitnessBrowser__HerbieS:HSERO_RS19990 270 VEKYQLKPRARILGMATAGVAPRIMGMGPAPASKKVLAQLGMTIDQMDVIELNEAFASQGLAVLRELG 337
                                                ******************************************************************** PP

                                  TIGR01930 326 sld.lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                  d +++vN nGGAiAlGHPlG+sGar+v+t  ++L++ g++y+l t+C+g GqG+A+++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS19990 338 VADdDARVNPNGGAIALGHPLGMSGARLVTTATYQLERTGGRYALCTMCIGVGQGIAMVIE 398
                                                86679******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (400 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: 9.47
//
[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