Alignments for a candidate for cysK in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Caulobacter crescentus NA1000

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate CCNA_03740 CCNA_03740 cysteine synthase

Query= BRENDA::C4ITG6
         (334 letters)



>FitnessBrowser__Caulo:CCNA_03740
          Length = 328

 Score =  424 bits (1090), Expect = e-123
 Identities = 213/314 (67%), Positives = 255/314 (81%), Gaps = 3/314 (0%)

Query: 22  AGRGRIYDSILDTIGNTPLVRIDKFARENGVKANLLVKLEFFNPLASVKDRIGLAMIEAL 81
           AGRG+IYDSI+DTIG+TPLVR+ + + E   KA +L KLEFFNP+ASVKDRIG++MIE+L
Sbjct: 16  AGRGKIYDSIIDTIGDTPLVRLPRLSAELNPKAEVLAKLEFFNPIASVKDRIGVSMIESL 75

Query: 82  EKQGKAVPGKTVFVEPTSGNTGIALAFAAAAKGYRLILTMPETMSMERRKLLRLLGAELV 141
           E QG   PG T+ +EPTSGNTGIALAF AAAKGY+L L MPE+MS+ERRK+L LLGA+L 
Sbjct: 76  EAQGVLKPGATI-IEPTSGNTGIALAFVAAAKGYKLTLVMPESMSIERRKMLLLLGAKLE 134

Query: 142 LTEGAKGMKGAIAEAEAI--GNPNAIIPQQFENPANPEIHRLTTAEEIWNDTNGEADILI 199
           LT   KGM+GA+  A+ +    P A++PQQFEN ANP IHR++TAEEIWNDT G  D ++
Sbjct: 135 LTPAEKGMRGAVTRAQELIEATPGAVMPQQFENSANPLIHRVSTAEEIWNDTAGAVDAVV 194

Query: 200 SGIGTGGTITGVGQVIKARKPSFKVVAVEPKDSPVLSGGAPGPHKIQGLGAGFAPKTLDT 259
           SG+GTGGTITGVGQ +KARKPS K+VAVEP+ SPVLSGGAPGPHKIQG+GAGF P  LD 
Sbjct: 195 SGVGTGGTITGVGQALKARKPSLKMVAVEPEASPVLSGGAPGPHKIQGIGAGFVPGVLDR 254

Query: 260 GIYDEIVQISNEDAFTNARLVARLEGIPVGISSGAALAAAIEVGKRSENAGKNIVVVIPS 319
           G+ D+IVQ+SN+DAF  AR  A  EG+PVGISSGAAL AA ++  R    GK IVV+IPS
Sbjct: 255 GVIDDIVQVSNDDAFAMARRAAATEGLPVGISSGAALTAAFDLALRDAYKGKTIVVIIPS 314

Query: 320 FAERYLSTALFEGL 333
           FAERYLSTALF+GL
Sbjct: 315 FAERYLSTALFDGL 328


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: 339
Number of extensions: 9
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: 334
Length of database: 328
Length adjustment: 28
Effective length of query: 306
Effective length of database: 300
Effective search space:    91800
Effective search space used:    91800
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 CCNA_03740 CCNA_03740 (cysteine synthase)
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.23607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-135  435.6   0.5   5.1e-135  435.4   0.5    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03740  CCNA_03740 cysteine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03740  CCNA_03740 cysteine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.4   0.5  5.1e-135  5.1e-135       3     298 .]      27     325 ..      25     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 435.4 bits;  conditional E-value: 5.1e-135
                             TIGR01139   3 eliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGial 72 
                                           ++iG+tPlvrL     + + kaevl+kle++nP +svkdri+++mie+ e +g+lk+g ti+e+tsGntGial
  lcl|FitnessBrowser__Caulo:CCNA_03740  27 DTIGDTPLVRLPrlsAELNPKAEVLAKLEFFNPIASVKDRIGVSMIESLEAQGVLKPGATIIEPTSGNTGIAL 99 
                                           79********987323445689*************************************************** PP

                             TIGR01139  73 amvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanp 145
                                           a+vaaa+gykl+l+mpe+ms+errk+l  +Ga+l Lt++++gm+ga+++a+el+e+tp   ++++qfen anp
  lcl|FitnessBrowser__Caulo:CCNA_03740 100 AFVAAAKGYKLTLVMPESMSIERRKMLLLLGAKLELTPAEKGMRGAVTRAQELIEATP-GAVMPQQFENSANP 171
                                           **********************************************************.556*********** PP

                             TIGR01139 146 eihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGig 218
                                            ihr +ta+ei++d+ g++da+v+gvGtGGtitGvg++lk  kp++k+vaveP++spvlsgg pgphkiqGig
  lcl|FitnessBrowser__Caulo:CCNA_03740 172 LIHRVSTAEEIWNDTAGAVDAVVSGVGTGGTITGVGQALKARKPSLKMVAVEPEASPVLSGGAPGPHKIQGIG 244
                                           ************************************************************************* PP

                             TIGR01139 219 agfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtge 290
                                           agf+P vLd+ vid++++vs+++a+++arr a+ eG+ vGissGaa+ aa  +a + + k+k+ivvi+p+++e
  lcl|FitnessBrowser__Caulo:CCNA_03740 245 AGFVPGVLDRGVIDDIVQVSNDDAFAMARRAAATEGLPVGISSGAALTAAFDLALRDAyKGKTIVVIIPSFAE 317
                                           ******************************************************99999************** PP

                             TIGR01139 291 rYlstaLf 298
                                           rYlstaLf
  lcl|FitnessBrowser__Caulo:CCNA_03740 318 RYLSTALF 325
                                           *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (328 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.81
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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