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 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__HerbieS:HSERO_RS01265
          Length = 398

 Score =  352 bits (902), Expect = e-101
 Identities = 191/393 (48%), Positives = 255/393 (64%), Gaps = 5/393 (1%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           +++A IV+  RTP+GKA +G     RPDDL    ++  + +  G +   I+D I+GC+ P
Sbjct: 5   LQDAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFP 64

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           E  QGLNMARN   LAGLP T+  +T+NRYC+SG+ +IA AA++I +G  D  IA GAES
Sbjct: 65  EGAQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAES 124

Query: 120 MSQVPMMGHVTRPNL-ALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAK 178
           MS VPMMG     N+ A  ++       MG TAE+VA+++ VSRE QD F++ SHQ A  
Sbjct: 125 MSMVPMMGFHPSININAFKDENVGMAYGMGLTAEKVAQQWKVSREAQDEFSLASHQKAIA 184

Query: 179 ALAEGKFKDEIVPVEVT--VTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSV 236
           A   G+F DE+   E+      +      ++ + V S DEG R  +    L+ L+P F+ 
Sbjct: 185 AQEAGEFADEMTSFEIVERFPNLATGEIDVKTRTV-SLDEGPRADSNLAALAKLKPVFAA 243

Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296
            G+VTAGNSSQTSDGA A++++  +      L PL +F SFAV GVPPE+MGIGP EAIP
Sbjct: 244 KGSVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIP 303

Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356
            ALK  GL    I   ELNEAFA+QA+ VI +LG+D  KVN  GGAIALGHPLG TG   
Sbjct: 304 AALKAGGLTQDQIDWIELNEAFAAQALAVIGDLGLDPSKVNPMGGAIALGHPLGATGAIR 363

Query: 357 TLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
             + IH ++R+N ++G+VTMC+G GMGAAG+FE
Sbjct: 364 AATTIHALRRKNLKYGMVTMCVGTGMGAAGIFE 396


Lambda     K      H
   0.316    0.133    0.377 

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: 412
Number of extensions: 15
Number of successful extensions: 4
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: 391
Length of database: 398
Length adjustment: 31
Effective length of query: 360
Effective length of database: 367
Effective search space:   132120
Effective search space used:   132120
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: 50 (23.9 bits)

Align candidate HSERO_RS01265 HSERO_RS01265 (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.19201.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.5e-141  456.2   5.4   5.1e-141  456.0   5.4    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS01265  HSERO_RS01265 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS01265  HSERO_RS01265 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.0   5.4  5.1e-141  5.1e-141       1     385 []      10     396 ..      10     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.0 bits;  conditional E-value: 5.1e-141
                                  TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaa 65 
                                                iv+a+Rtpig + +g +k+++++dLl+ +i+++++++ gldp+ i+++i+G+++++g+q  n+aR+a+
  lcl|FitnessBrowser__HerbieS:HSERO_RS01265  10 IVAATRTPIGkAPRGMFKNTRPDDLLVRAIQSAVAQVpGLDPKLIEDAIVGCSFPEGAQgLNMARNAV 77 
                                                8*********988******************************************************* PP

                                  TIGR01930  66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgk 133
                                                l aglp+++ ++t+nr+CaSg++A+a+aa++i++Geadv++a+G+EsmS vp++  +     s+++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01265  78 LLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAESMSMVPMMGFH----PSININA 141
                                                ****************************************************96665....5899999 PP

                                  TIGR01930 134 akledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk 201
                                                +k+e+      v  ++ mg tAe++a+++++sRe qDe++l+Shqka +A+e+g+f+de + +e+ ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01265 142 FKDEN------VGMAYGMGLTAEKVAQQWKVSREAQDEFSLASHQKAIAAQEAGEFADEMTSFEIVER 203
                                                99999......6779***************************************************99 PP

                                  TIGR01930 202 ............kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseev 257
                                                            +++vs Deg+r++++l++LakLkp+f+  kgs vtAgNssq++DGA+al+++se++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01265 204 fpnlatgeidvkTRTVSLDEGPRADSNLAALAKLKPVFAA-KGS-VTAGNSSQTSDGAGALIIVSEKI 269
                                                ***********999************************96.8*7.*********************** PP

                                  TIGR01930 258 akelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelg 325
                                                +k+++ltplar+vs+av gv+pe+mg+gp +Ai++aLk  gl+ ++id++E+nEAFAaq+lav+ +lg
  lcl|FitnessBrowser__HerbieS:HSERO_RS01265 270 LKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIPAALKAGGLTQDQIDWIELNEAFAAQALAVIGDLG 337
                                                ******************************************************************** PP

                                  TIGR01930 326 sldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                 ld++kvN  GGAiAlGHPlGa+Ga+  +t++++L++++ kyG++t+Cvg+G+GaA i+e
  lcl|FitnessBrowser__HerbieS:HSERO_RS01265 338 -LDPSKVNPMGGAIALGHPLGATGAIRAATTIHALRRKNLKYGMVTMCVGTGMGAAGIFE 396
                                                .99******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (398 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: 9.15
//
[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