Alignments for a candidate for cysK in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Desulfuromusa kysingii DSM 7343

Align Cysteine synthase; CSase; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase; EC 2.5.1.47 (characterized)
to candidate WP_175498371.1 BLU87_RS11865 cysteine synthase A

Query= SwissProt::Q59966
         (329 letters)



>NCBI__GCF_900107645.1:WP_175498371.1
          Length = 324

 Score =  438 bits (1127), Expect = e-128
 Identities = 218/310 (70%), Positives = 260/310 (83%)

Query: 8   FADNSQTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAEQRGLLGP 67
           +ADN+ +IG+TPLVRLN+I+    A V  KIEGRNPAYSVKCRIG +MI DA Q+G L P
Sbjct: 14  YADNTLSIGRTPLVRLNKIIGSGRAQVYGKIEGRNPAYSVKCRIGVSMIQDALQKGTLKP 73

Query: 68  GKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGVKGMT 127
           G E++EPTSGNTGIALAFVAAA+GIPLTLTMPETMSLERRK+L A+GAKL+LT G KGM 
Sbjct: 74  GMEIVEPTSGNTGIALAFVAAAKGIPLTLTMPETMSLERRKVLKAFGAKLILTSGGKGMA 133

Query: 128 GAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVSGVGTGGT 187
           GAV  AE +A   P+RY+LL QF+NPANP IH +TTGPEIWEDT G +D+LV+GVGTGGT
Sbjct: 134 GAVHEAEQMAEEYPERYLLLHQFKNPANPEIHAKTTGPEIWEDTDGNVDVLVAGVGTGGT 193

Query: 188 ITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFIPENLDLS 247
           I+G+S++IK+ + K +++VAVEPE SPVISQ  +G  L+PGPHKIQGIGAGFIPE LDL+
Sbjct: 194 ISGISKFIKEEKNKALMTVAVEPEDSPVISQHLAGEMLQPGPHKIQGIGAGFIPETLDLA 253

Query: 248 LVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTIVVVLPDS 307
           LVD VE VSN+EA  YARRLA+EEG++SGIS GAA A A RL++Q E AGK IVV+LPDS
Sbjct: 254 LVDHVELVSNDEAYEYARRLAREEGILSGISSGAAAAVAARLSKQPELAGKNIVVILPDS 313

Query: 308 GERYLSTALF 317
           GERYLS+ LF
Sbjct: 314 GERYLSSDLF 323


Lambda     K      H
   0.316    0.134    0.378 

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: 409
Number of extensions: 16
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: 329
Length of database: 324
Length adjustment: 28
Effective length of query: 301
Effective length of database: 296
Effective search space:    89096
Effective search space used:    89096
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: 48 (23.1 bits)

Align candidate WP_175498371.1 BLU87_RS11865 (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.1523158.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-137  444.0   0.2   1.4e-137  443.8   0.2    1.0  1  NCBI__GCF_900107645.1:WP_175498371.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900107645.1:WP_175498371.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.8   0.2  1.4e-137  1.4e-137       3     298 .]      19     323 ..      17     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 443.8 bits;  conditional E-value: 1.4e-137
                             TIGR01139   3 eliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialam 74 
                                             iG+tPlvrLn ++ + +a+v+ k+e +nP++svk+ri+++mi+da ++g+lk+g +ive+tsGntGiala+
  NCBI__GCF_900107645.1:WP_175498371.1  19 LSIGRTPLVRLNkIIGSGRAQVYGKIEGRNPAYSVKCRIGVSMIQDALQKGTLKPGMEIVEPTSGNTGIALAF 91 
                                           68**********7777789****************************************************** PP

                             TIGR01139  75 vaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpei 147
                                           vaaa+g  l+ltmpetmslerrk+lka+Ga+l+Lt g +gm+ga+++ae+++ee p++ylll+qf+npanpei
  NCBI__GCF_900107645.1:WP_175498371.1  92 VAAAKGIPLTLTMPETMSLERRKVLKAFGAKLILTSGGKGMAGAVHEAEQMAEEYPERYLLLHQFKNPANPEI 164
                                           ************************************************************************* PP

                             TIGR01139 148 hrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphk 213
                                           h ktt+pei++d+dg++d++vagvGtGGti+G+++ +ke+k+  +  vaveP++spv+s+       +pgphk
  NCBI__GCF_900107645.1:WP_175498371.1 165 HAKTTGPEIWEDTDGNVDVLVAGVGTGGTISGISKFIKEEKNkALMTVAVEPEDSPVISQHlagemlQPGPHK 237
                                           **************************************99986899**************999********** PP

                             TIGR01139 214 iqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvil 285
                                           iqGigagfiP+ Ld  ++d+v  vs++ea+e+arrla+eeGil+GissGaa a a +++k++e ++k+ivvil
  NCBI__GCF_900107645.1:WP_175498371.1 238 IQGIGAGFIPETLDLALVDHVELVSNDEAYEYARRLAREEGILSGISSGAAAAVAARLSKQPElAGKNIVVIL 310
                                           ************************************************************************* PP

                             TIGR01139 286 pdtgerYlstaLf 298
                                           pd+gerYls +Lf
  NCBI__GCF_900107645.1:WP_175498371.1 311 PDSGERYLSSDLF 323
                                           ***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (324 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.19
//
[ok]

This GapMind analysis is from Jul 25 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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis