GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Phyllobacterium endophyticum PEPV15

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_106716171.1 CU100_RS08500 cysteine synthase A

Query= BRENDA::C4ITG6
         (334 letters)



>NCBI__GCF_003010935.1:WP_106716171.1
          Length = 324

 Score =  503 bits (1294), Expect = e-147
 Identities = 252/325 (77%), Positives = 287/325 (88%), Gaps = 6/325 (1%)

Query: 14  LGSKDAEAAGRGRIYDSILDTIGNTPLVRIDKFARENGVKANLLVKLEFFNPLASVKDRI 73
           + S+     GRGRIY+SI+DTIG+TPL+R+DK A+E GV ANLL KLEFFNP++SVKDRI
Sbjct: 1   MSSESVRKPGRGRIYNSIVDTIGDTPLIRLDKLAKEKGVGANLLAKLEFFNPISSVKDRI 60

Query: 74  GLAMIEALEKQGKAVPGKTVFVEPTSGNTGIALAFAAAAKGYRLILTMPETMSMERRKLL 133
           G+A+IEALE QG+A PGKT  +EPTSGNTGIALAFAAAAKGYRLILTMPETMS+ERRK+L
Sbjct: 61  GVALIEALEVQGRATPGKTTLIEPTSGNTGIALAFAAAAKGYRLILTMPETMSVERRKML 120

Query: 134 RLLGAELVLTEGAKGMKGAIAEA----EAIGNPNAIIPQQFENPANPEIHRLTTAEEIWN 189
           +LLGAELVLTEGAKGMKGAIA+A    E IG+  A+IP QF+NPANPEIHR TTAEEIWN
Sbjct: 121 KLLGAELVLTEGAKGMKGAIAKANELVETIGD--AVIPGQFDNPANPEIHRRTTAEEIWN 178

Query: 190 DTNGEADILISGIGTGGTITGVGQVIKARKPSFKVVAVEPKDSPVLSGGAPGPHKIQGLG 249
           DT G  DIL++GIGTGGTITGVGQV+K RKP   VVAVEPKDSP+LSGG PGPHKIQG+G
Sbjct: 179 DTEGSVDILVAGIGTGGTITGVGQVLKQRKPGVLVVAVEPKDSPILSGGNPGPHKIQGIG 238

Query: 250 AGFAPKTLDTGIYDEIVQISNEDAFTNARLVARLEGIPVGISSGAALAAAIEVGKRSENA 309
           AGFAP  LDT IYDE+VQ+SNED+F NARLVAR+EG+PVGISSGAAL AAIEVG+R EN 
Sbjct: 239 AGFAPAVLDTHIYDEVVQVSNEDSFANARLVARIEGVPVGISSGAALTAAIEVGQRPENK 298

Query: 310 GKNIVVVIPSFAERYLSTALFEGLE 334
           GKN+VV+IPSFAERYLSTALFEGL+
Sbjct: 299 GKNLVVIIPSFAERYLSTALFEGLD 323


Lambda     K      H
   0.314    0.134    0.373 

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: 417
Number of extensions: 6
Number of successful extensions: 2
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: 334
Length of database: 324
Length adjustment: 28
Effective length of query: 306
Effective length of database: 296
Effective search space:    90576
Effective search space used:    90576
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: 42 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_106716171.1 CU100_RS08500 (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.3199456.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-135  434.8   1.3   9.2e-135  434.6   1.3    1.0  1  NCBI__GCF_003010935.1:WP_106716171.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106716171.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.6   1.3  9.2e-135  9.2e-135       2     298 .]      19     319 ..      18     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.6 bits;  conditional E-value: 9.2e-135
                             TIGR01139   2 seliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveatsGntGi 70 
                                            ++iG+tPl+rL+    ++++ a++l+kle++nP ssvkdri++a+ie  e +g  ++gk t++e+tsGntGi
  NCBI__GCF_003010935.1:WP_106716171.1  19 VDTIGDTPLIRLDklaKEKGVGANLLAKLEFFNPISSVKDRIGVALIEALEVQGRATPGKtTLIEPTSGNTGI 91 
                                           589*********98544567789************************************989*********** PP

                             TIGR01139  71 alamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpa 143
                                           ala+ aaa+gy+liltmpetms+errk+lk +GaelvLt+ga+gmkgai+ka+elve+ +++  ++ qf+npa
  NCBI__GCF_003010935.1:WP_106716171.1  92 ALAFAAAAKGYRLILTMPETMSVERRKMLKLLGAELVLTEGAKGMKGAIAKANELVETIGDAV-IPGQFDNPA 163
                                           ************************************************************776.********* PP

                             TIGR01139 144 npeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqG 216
                                           npeihr+tta+ei++d++g++d++vag+GtGGtitGvg+vlk+ kp + vvaveP++sp+lsgg+pgphkiqG
  NCBI__GCF_003010935.1:WP_106716171.1 164 NPEIHRRTTAEEIWNDTEGSVDILVAGIGTGGTITGVGQVLKQRKPGVLVVAVEPKDSPILSGGNPGPHKIQG 236
                                           ************************************************************************* PP

                             TIGR01139 217 igagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdt 288
                                           igagf P+vLd++++dev++vs+e++++ ar +a+ eG+ vGissGaa+ aa++v +++e k+k++vvi+p++
  NCBI__GCF_003010935.1:WP_106716171.1 237 IGAGFAPAVLDTHIYDEVVQVSNEDSFANARLVARIEGVPVGISSGAALTAAIEVGQRPEnKGKNLVVIIPSF 309
                                           ***********************************************************99************ PP

                             TIGR01139 289 gerYlstaLf 298
                                           +erYlstaLf
  NCBI__GCF_003010935.1:WP_106716171.1 310 AERYLSTALF 319
                                           *********9 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.67
//
[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