Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate Ga0059261_3284 Ga0059261_3284 acetyl-CoA acetyltransferases

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__Korea:Ga0059261_3284
          Length = 391

 Score =  318 bits (816), Expect = 1e-91
 Identities = 176/393 (44%), Positives = 251/393 (63%), Gaps = 6/393 (1%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M+ AVIVS ARTP+G+A +G+   +    L A  ++  ++RAG   G + D++ G A  +
Sbjct: 1   MRSAVIVSTARTPIGRAYRGAFNALPAQTLAARSIEAAVQRAGIEGGEVQDVVFGAALQQ 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
             Q  N+AR     AGLP +V  ++V+R C+SGL +IA AA++I++   D AI GG ES+
Sbjct: 61  GHQAGNIARQAALRAGLPVSVSGMSVDRQCASGLMAIATAAKQIIVDNMDIAIGGGVESI 120

Query: 121 S--QVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAK 178
           S  Q P M     P L       + YM M  TAE VA +Y +SRE QD ++++S Q  A 
Sbjct: 121 SLVQTPQMRIAADPELLAMHN--DVYMPMLQTAEVVAARYNISREVQDEYSLQSQQRTAA 178

Query: 179 ALAEGKFKDEIVPVEVTVTEIGEDHKPM-EKQFVFSQDEGVRPQTTADILSTLRPAFSVD 237
           A A GKF DEIVPV  T+  + ++ K + +K+   ++DEG RP+TT + L  L+P    +
Sbjct: 179 AQAAGKFDDEIVPVTATMNIVNKETKEVTQKEVTLTKDEGNRPETTLEGLQALQPVVP-N 237

Query: 238 GTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPR 297
           G +TAGN+SQ SDG+++ +LM+ + A+  GL PL ++   AV G  P+ MGIGPV AIP 
Sbjct: 238 GVITAGNASQLSDGSSSSVLMEEKLAEKRGLTPLGRYVGMAVAGTKPDEMGIGPVFAIPA 297

Query: 298 ALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLT 357
            L+   L++ DIGL+ELNEAFA Q +    +LGI  E +NVNGG+I++GHP G TG + T
Sbjct: 298 LLERFNLKMDDIGLWELNEAFAVQVLYCRDKLGIPNELLNVNGGSISIGHPYGMTGARCT 357

Query: 358 LSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
              + E KRR  ++ VVTMC+GGGMGAAG+FE+
Sbjct: 358 GHALIEGKRRGAKYVVVTMCVGGGMGAAGLFEV 390


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: 399
Number of extensions: 12
Number of successful extensions: 5
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: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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 Ga0059261_3284 Ga0059261_3284 (acetyl-CoA acetyltransferases)
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.26218.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-128  413.5   6.4   4.7e-128  413.3   6.4    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3284  Ga0059261_3284 acetyl-CoA acetyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3284  Ga0059261_3284 acetyl-CoA acetyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.3   6.4  4.7e-128  4.7e-128       1     385 []       6     389 ..       6     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 413.3 bits;  conditional E-value: 4.7e-128
                                 TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaala 67 
                                               iv+++Rtpig +++g+++ l+a++L+a  i+++++rag++  ++ +v++G++lq+g+q  niaR+aal+
  lcl|FitnessBrowser__Korea:Ga0059261_3284   6 IVSTARTPIGrAYRGAFNALPAQTLAARSIEAAVQRAGIEGGEVQDVVFGAALQQGHQaGNIARQAALR 74 
                                               89*********99*********************************************9********** PP

                                 TIGR01930  68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136
                                               aglp sv++++v+r+CaSgl A+a+aa++i + ++d+++ GGvEs+S v    ++   r  ++++   +
  lcl|FitnessBrowser__Korea:Ga0059261_3284  75 AGLPVSVSGMSVDRQCASGLMAIATAAKQIIVDNMDIAIGGGVESISLVQT--PQ--MRIAADPELLAM 139
                                               ***********************************************9964..33..367888888888 PP

                                 TIGR01930 137 edqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.... 201
                                               ++       +  ++m +tAe +a++y+isRe qDey+l+S+q++a+A+++gkf+deivpv+   +    
  lcl|FitnessBrowser__Korea:Ga0059261_3284 140 HN-------DVYMPMLQTAEVVAARYNISREVQDEYSLQSQQRTAAAQAAGKFDDEIVPVTATMNivnk 201
                                               88.......6779************************************************99989999 PP

                                 TIGR01930 202 ........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelg 262
                                                       +++++kDeg rp+ttle L+ L+p+   ++g ++tAgN+sql+DG++  +lm+e+ a++ g
  lcl|FitnessBrowser__Korea:Ga0059261_3284 202 etkevtqkEVTLTKDEGNRPETTLEGLQALQPVV--PNG-VITAGNASQLSDGSSSSVLMEEKLAEKRG 267
                                               ******99999***********************..489.7**************************** PP

                                 TIGR01930 263 ltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlek 331
                                               ltpl+r+v++avag +p+emg+gpv Ai+++L++ +l+++di l+E+nEAFA+qvl+++++lg + +e 
  lcl|FitnessBrowser__Korea:Ga0059261_3284 268 LTPLGRYVGMAVAGTKPDEMGIGPVFAIPALLERFNLKMDDIGLWELNEAFAVQVLYCRDKLG-IPNEL 335
                                               ***************************************************************.889** PP

                                 TIGR01930 332 vNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +NvnGG+i++GHP+G++Gar++ + l e k+rg+ky ++t+CvggG+GaA ++e
  lcl|FitnessBrowser__Korea:Ga0059261_3284 336 LNVNGGSISIGHPYGMTGARCTGHALIEGKRRGAKYVVVTMCVGGGMGAAGLFE 389
                                               **************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.12
//
[ok]

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

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Protein sequences (fasta format)
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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