GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Sinorhizobium fredii NGR234

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_012709489.1 NGR_RS26100 acetyl-CoA C-acyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982
         (397 letters)



>NCBI__GCF_000018545.1:WP_012709489.1
          Length = 393

 Score =  479 bits (1232), Expect = e-140
 Identities = 251/395 (63%), Positives = 306/395 (77%), Gaps = 4/395 (1%)

Query: 3   MSN-DPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVL 61
           MSN DP+VIVSA RTPMG FQG LK LTAP+LGA A+KAA++RAG+  D+VDEV+ G VL
Sbjct: 1   MSNRDPVVIVSAARTPMGAFQGGLKDLTAPELGAIALKAALDRAGL--DAVDEVMMGNVL 58

Query: 62  PAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMES 121
           PAGLGQ PARQAALGAGL + T  TT++K+CGSGM+A +L HD L++GSA VV  GGMES
Sbjct: 59  PAGLGQNPARQAALGAGLGQQTPSTTVSKVCGSGMKALMLGHDALISGSASVVGVGGMES 118

Query: 122 MSNAPYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQD 181
           M+NAPYLL +AR G+R+GHG V+D MFLDGLEDAY  GRLMGT+AED A+   FSR  QD
Sbjct: 119 MTNAPYLLPKARGGFRLGHGEVKDHMFLDGLEDAYS-GRLMGTYAEDTAQHYQFSRADQD 177

Query: 182 AFAIASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFRE 241
           AFA+ S  RA +A +D SF  EIV +T    +    +  DEQP KA   KI  LKPAFR+
Sbjct: 178 AFALRSLERALKAAEDKSFADEIVAITDGGKRGTANLDRDEQPTKADPAKIPKLKPAFRD 237

Query: 242 GGTVTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIK 301
           GG+VTAANSSSISDGAAALVLMR S+A+++GL PLA++ GHA  A  P  F  APIGAI 
Sbjct: 238 GGSVTAANSSSISDGAAALVLMRASEAERRGLTPLAIVAGHAGHAQEPAWFTTAPIGAID 297

Query: 302 KLMKKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARI 361
           KL++K GW    V L E+NEAFA+V MAA+  L +  + +N+HGGACALGHPIGASGARI
Sbjct: 298 KLIEKLGWEKGSVGLYEINEAFAIVAMAAIRDLGLSDDIVNIHGGACALGHPIGASGARI 357

Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVECL 396
           +VTLL A+R  G+KRG+A++CIGGGEATA+ +E +
Sbjct: 358 VVTLLHAMRANGVKRGIASLCIGGGEATAVGLELM 392


Lambda     K      H
   0.318    0.132    0.376 

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: 587
Number of extensions: 21
Number of successful extensions: 3
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: 397
Length of database: 393
Length adjustment: 31
Effective length of query: 366
Effective length of database: 362
Effective search space:   132492
Effective search space used:   132492
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 WP_012709489.1 NGR_RS26100 (acetyl-CoA C-acyltransferase)
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.1071391.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-121  390.3   3.6   5.1e-121  390.2   3.6    1.0  1  NCBI__GCF_000018545.1:WP_012709489.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012709489.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.2   3.6  5.1e-121  5.1e-121       1     384 [.       9     389 ..       9     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 390.2 bits;  conditional E-value: 5.1e-121
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a+Rtp+g+++g lk+l+a +L+a ++k++l+ragld  ++dev++Gnvl+ag ++n+aR+aal agl+++
  NCBI__GCF_000018545.1:WP_012709489.1   9 IVSAARTPMGAFQGGLKDLTAPELGAIALKAALDRAGLD--AVDEVMMGNVLPAGLGQNPARQAALGAGLGQQ 79 
                                           8*************************************9..6******************************* PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           +p++tv++vC+Sg++A++l+ +++ +G a+vv +GG+Esm+++p+ll+++  r +++lg+ +++d++  d+  
  NCBI__GCF_000018545.1:WP_012709489.1  80 TPSTTVSKVCGSGMKALMLGHDALISGSASVVGVGGMESMTNAPYLLPKA--RGGFRLGHGEVKDHMFLDGle 150
                                           ************************************************98..89***********99999999 PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            ++++  mg+ Ae +a++y++sR +qD++alrS ++a kA e++ f+deiv ++  gk  +  +++De++  +
  NCBI__GCF_000018545.1:WP_012709489.1 151 dAYSGRLMGTYAEDTAQHYQFSRADQDAFALRSLERALKAAEDKSFADEIVAITDGGKrgTANLDRDEQPT-K 222
                                           988999*************************************************9999988999999998.7 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                              +k+ kLkpaf++  gs vtA+Nss+++DGAaal+lm  + a++ gltpla + ++a  + +p+ ++++p+
  NCBI__GCF_000018545.1:WP_012709489.1 223 ADPAKIPKLKPAFRD-GGS-VTAANSSSISDGAAALVLMRASEAERRGLTPLAIVAGHAGHAQEPAWFTTAPI 293
                                           899**********96.786.***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                            Ai k+++k g++  ++ l+EinEAFA +++a++++lg l+++ vN++GGA AlGHP+GasGariv+tll+++
  NCBI__GCF_000018545.1:WP_012709489.1 294 GAIDKLIEKLGWEKGSVGLYEINEAFAIVAMAAIRDLG-LSDDIVNIHGGACALGHPIGASGARIVVTLLHAM 365
                                           **************************************.889******************************* PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvil 384
                                           + +g+k+G+a+lC+ggG ++Av l
  NCBI__GCF_000018545.1:WP_012709489.1 366 RANGVKRGIASLCIGGGEATAVGL 389
                                           *********************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 00:00:00.00
# Mc/sec: 17.22
//
[ok]

This GapMind analysis is from Apr 09 2024. 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