GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Phyllobacterium endophyticum PEPV15

Align O-ureido-L-serine synthase; Cysteine synthase homolog DscD; O-acetylserine sulfhydrylase; EC 2.6.99.3; EC 2.5.1.47 (characterized)
to candidate WP_106717134.1 CU100_RS14020 cysteine synthase A

Query= SwissProt::D2Z027
         (324 letters)



>NCBI__GCF_003010935.1:WP_106717134.1
          Length = 362

 Score =  317 bits (812), Expect = 3e-91
 Identities = 169/330 (51%), Positives = 216/330 (65%), Gaps = 20/330 (6%)

Query: 3   LFNSILDTIGRTPIVRLQRMAPEHTSVYVKVESFNPGGSVKDRLALSVVLDAEAKGLLKP 62
           LF+SILDTIG TP VR+  +AP+H ++YVK E FNP  SVKDRLAL+++ +AE  G LKP
Sbjct: 16  LFDSILDTIGDTPAVRINNLAPDHVTIYVKAEFFNPASSVKDRLALNIIEEAERNGTLKP 75

Query: 63  GDTIVECTSGNVGIALAMVAAARGYRFVAVMGDTYSVERRKLIRAYGGKLVLFPGHLGSK 122
           G T+VE TSGN GI LAMV A +GY  V  M D++S+ERRKL+R  G K+VL P      
Sbjct: 76  GQTVVEATSGNTGIGLAMVCAQKGYPLVVTMADSFSIERRKLMRMLGAKVVLTPRAQKGF 135

Query: 123 GGNLIADELAEKYGWFRARQFDNPANPSYHRETTASEILADFAGKRLDHFVTGFGTTGTL 182
           G    A ELAE  GWF ARQF+  AN   H  TTA EI+ DFAG RLD+FVTG+GT GT+
Sbjct: 136 GMYQKAVELAEMNGWFLARQFETEANADIHEATTAREIINDFAGSRLDYFVTGYGTGGTV 195

Query: 183 TGVGQMLRVARPEVRVVALEPSNAAMLARGE----------------WSPHQIQGLAPNF 226
           +GVG++LR  RPE R+V  EP+NA +L  G+                + PH IQG  P+F
Sbjct: 196 SGVGRVLRRERPETRIVLSEPANAQLLGSGKVQVRGAGGAPAASHPAFEPHPIQGWTPDF 255

Query: 227 VPGVL----DRSVIDDLVTMDEVTARDTSRRLAAEEGIFAGISAGATVATALSIAEHAPE 282
           +P VL    D  + D ++ +        +R LA +EG+F GIS GAT A A SIAE A  
Sbjct: 256 IPNVLQEAIDHKLYDQVMPIAGPEGIKWARALAQKEGMFTGISGGATFAVAHSIAETAAA 315

Query: 283 GTVLLAMLPDTGERYLSTFLFDGVDEGSDD 312
           G+V+L MLPDTGERY++T LF+G++   D+
Sbjct: 316 GSVILCMLPDTGERYMTTPLFEGIETEMDE 345


Lambda     K      H
   0.319    0.136    0.395 

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: 317
Number of extensions: 13
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: 324
Length of database: 362
Length adjustment: 29
Effective length of query: 295
Effective length of database: 333
Effective search space:    98235
Effective search space used:    98235
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_106717134.1 CU100_RS14020 (cysteine synthase A)
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

# 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.aa/TIGR01139.hmm
# target sequence database:        /tmp/gapView.3980528.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01139  [M=298]
Accession:   TIGR01139
Description: cysK: cysteine synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-110  353.3   0.0   6.5e-110  353.0   0.0    1.1  1  NCBI__GCF_003010935.1:WP_106717134.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106717134.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.0   0.0  6.5e-110  6.5e-110       2     298 .]      21     336 ..      20     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 353.0 bits;  conditional E-value: 6.5e-110
                             TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialam 74 
                                            ++iG+tP vr+n  ++ ++ ++vk e++nP+ssvkdr+al++ie+ae++g+lk+g+t+veatsGntGi+lam
  NCBI__GCF_003010935.1:WP_106717134.1  21 LDTIGDTPAVRINNLAPDHVTIYVKAEFFNPASSVKDRLALNIIEEAERNGTLKPGQTVVEATSGNTGIGLAM 93 
                                           579**********99999******************************************************* PP

                             TIGR01139  75 vaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpei 147
                                           v+a++gy l++tm++++s+errkl++++Ga++vLt+ a++  g+ +ka el+e ++  ++l++qfe +an +i
  NCBI__GCF_003010935.1:WP_106717134.1  94 VCAQKGYPLVVTMADSFSIERRKLMRMLGAKVVLTPRAQKGFGMYQKAVELAEMNG--WFLARQFETEANADI 164
                                           *******************************************************9..99************* PP

                             TIGR01139 148 hrkttapeilkdldgk.ldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsgg............ 207
                                           h++tta+ei++d+ g+ ld fv+g+GtGGt++Gvg+vl++++p+ ++v +ePa++++l  g            
  NCBI__GCF_003010935.1:WP_106717134.1 165 HEATTAREIINDFAGSrLDYFVTGYGTGGTVSGVGRVLRRERPETRIVLSEPANAQLLGSGkvqvrgaggapa 237
                                           *************9988*****************************************8888*********** PP

                             TIGR01139 208 ....kpgphkiqGigagfiPkvL....dkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkva 272
                                                  ph iqG++++fiP+vL    d++++d+v+ +   e i+ ar la++eG+++Gis+Ga+ a a  +a
  NCBI__GCF_003010935.1:WP_106717134.1 238 ashpAFEPHPIQGWTPDFIPNVLqeaiDHKLYDQVMPIAGPEGIKWARALAQKEGMFTGISGGATFAVAHSIA 310
                                           *988889**************9844446789****************************************** PP

                             TIGR01139 273 kklekdkkivvilpdtgerYlstaLf 298
                                           + ++++ +i+++lpdtgerY++t+Lf
  NCBI__GCF_003010935.1:WP_106717134.1 311 ETAAAGSVILCMLPDTGERYMTTPLF 336
                                           *************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (362 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: 00:00:00.00
# Mc/sec: 16.01
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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