Alignments for a candidate for cimA in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Nitriliruptor alkaliphilus DSM 45188

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_052669621.1 NITAL_RS11655 citramalate synthase

Query= BRENDA::B0K6M2
         (520 letters)



>NCBI__GCF_000969705.1:WP_052669621.1
          Length = 556

 Score =  425 bits (1093), Expect = e-123
 Identities = 223/527 (42%), Positives = 324/527 (61%), Gaps = 18/527 (3%)

Query: 6   IYDTTLRDGVQGQGISFTVEDKLKIVKVLDEFGVAYIEAGNPGSNPKDIEFFERVKNIKL 65
           +YDTTLRDG Q +G++ +V+DKL++ + +DE GVAYIE G PG+NPKD EFF R    +L
Sbjct: 17  LYDTTLRDGTQREGVTLSVDDKLRVARRMDELGVAYIEGGWPGANPKDTEFFRRAAEGEL 76

Query: 66  K-NAKLIAFGSTRRANTTTEEDANVISLLNADTEVVTIFGKSWDFQVTEILKTTLEENLK 124
              A L+AFG TR  N   E+D  +  L+ A T+V+ + GKSW + V E L    +ENL 
Sbjct: 77  DLAATLVAFGMTRGPNRAAEDDVLLQGLVEARTDVICLVGKSWGYHVDEALGVPRDENLA 136

Query: 125 MIYDTVKFFKDKGKSVIFDAEHFFDGYKQNPEYALKTLEVALEAGVDSVCLCDTKGGAFP 184
           M+ D++ + +  GK V FDAEHFFDG  ++  YA   + VA EAG + V LCDT GGA P
Sbjct: 137 MVRDSITYLRGLGKRVFFDAEHFFDGLARDGAYARDVVRVAAEAGAECVVLCDTNGGAMP 196

Query: 185 MEVYDITKTVVDKFNTEVGIHCHNDNGMAVADSIMAVQAGAIQLQGTINGYGERCGNANL 244
            +V +I + +V     +VG+H H+D G AVA+S++ V+AGA+ +QGT NG GERCGNANL
Sbjct: 197 WDVLEIVRGLVHDLPCDVGLHFHDDGGCAVANSMLGVEAGAVHVQGTANGLGERCGNANL 256

Query: 245 CTLIPNLQLLMGYKCVPDENLKQLTHLARFVSEIANVTYDERAPYVGKNAFSHKAGMHAD 304
            T++ +LQL  G   +  E L++LT ++  V+E+ N    + APYVG  AFSHKAG+HA 
Sbjct: 257 FTIVADLQLKRGLPLIAPEQLERLTEISHTVAELCNQATPDVAPYVGHTAFSHKAGLHAS 316

Query: 305 AVNKNTYSYELIDPSLVGNSRTFLISEVAGRGAVLNAINEIDPTITKDSPETKLILDKLK 364
           A+ K    Y+ I+P  VGN +  ++SE+AGR  ++    E+   +T D  + K +L ++K
Sbjct: 317 ALAKAPDMYQHIEPDDVGNRQRLVVSELAGRSNIVLKAKELGVDVTAD--QAKAVLAEVK 374

Query: 365 EMEYLGYQYENAGGSLELLIRKVLG---KYKPAFNLKEFKVIVNEPSVNSVN----SSAL 417
             E LG+ YE A  S  LL+R+V G        F    ++V V   +  + N    + A+
Sbjct: 375 RRESLGWTYEAADASFGLLLRRVAGLLADEDEPFRSLHYRVNVGGGAAEATNGEGPAEAI 434

Query: 418 IKVEVDSIEEIAAAEGDGPVHALDNAVRRVLERFYPQIKEMRLTDYKVRVLDSNSATA-- 475
           + VEV  +  + A EG+GPV ALD+A R  +   +P +  + L DYKVR+L++ SAT   
Sbjct: 435 LAVEVAGVRRLGAGEGNGPVDALDHAFRNAVNGTWPDLDRVHLADYKVRILEAVSATGDR 494

Query: 476 ------AKVRVIIESTDGKDSWSTIGVSTDIIEASWRALVDSIEYKL 516
                 A  RV++ +TDG   W T+GV  +++EASW AL D+  + +
Sbjct: 495 DGIGTDAVTRVLVTATDGTTKWDTVGVHANVVEASWLALSDAYTHAI 541


Lambda     K      H
   0.316    0.134    0.377 

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: 657
Number of extensions: 25
Number of successful extensions: 5
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: 520
Length of database: 556
Length adjustment: 35
Effective length of query: 485
Effective length of database: 521
Effective search space:   252685
Effective search space used:   252685
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: 52 (24.6 bits)

Align candidate WP_052669621.1 NITAL_RS11655 (citramalate synthase)
to HMM TIGR00977 (cimA: citramalate synthase (EC 2.3.1.182))

# 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/TIGR00977.hmm
# target sequence database:        /tmp/gapView.30984.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00977  [M=526]
Accession:   TIGR00977
Description: citramal_synth: citramalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-179  583.7   0.0   1.7e-179  583.3   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052669621.1  NITAL_RS11655 citramalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052669621.1  NITAL_RS11655 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.3   0.0  1.7e-179  1.7e-179       2     514 ..      15     538 ..      14     543 .. 0.94

  Alignments for each domain:
  == domain 1  score: 583.3 bits;  conditional E-value: 1.7e-179
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlk.nakvv 69 
                                               l lydttlrdG+q+eGv+ls++dk+r+a+++d+lG+ yieGGwpganpkd++ff+++ e +l+  a +v
  lcl|NCBI__GCF_000969705.1:WP_052669621.1  15 LDLYDTTLRDGTQREGVTLSVDDKLRVARRMDELGVAYIEGGWPGANPKDTEFFRRAAEGELDlAATLV 83 
                                               679********************************************************999835789* PP

                                 TIGR00977  70 afsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadev 138
                                               af+ tr p+++ e+d  lq l++a t v+ + Gksw  hv eal    +enl+m+ d+++yl+  +++v
  lcl|NCBI__GCF_000969705.1:WP_052669621.1  84 AFGMTRGPNRAAEDDVLLQGLVEARTDVICLVGKSWGYHVDEALGVPRDENLAMVRDSITYLRGLGKRV 152
                                               ********************************************************************* PP

                                 TIGR00977 139 iydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahn 207
                                                +daehffdG   +  ya ++++va +aGa+++vl+dtnGG++p ++ ei++ + + l    +G+h h+
  lcl|NCBI__GCF_000969705.1:WP_052669621.1 153 FFDAEHFFDGLARDGAYARDVVRVAAEAGAECVVLCDTNGGAMPWDVLEIVRGLVHDLPCD-VGLHFHD 220
                                               *****************************************************99999765.******* PP

                                 TIGR00977 208 dsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvae 276
                                               d + avans+l veaGav+vqGt nGlGercGnanl +++ +lqlk gl +i +e+l++lte+++ vae
  lcl|NCBI__GCF_000969705.1:WP_052669621.1 221 DGGCAVANSMLGVEAGAVHVQGTANGLGERCGNANLFTIVADLQLKRGLPLIAPEQLERLTEISHTVAE 289
                                               ********************************************************************* PP

                                 TIGR00977 277 ivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelG 345
                                               + n+a+++ +pyvG++af+hk G+h+sa+ + p  y+hi+p+ vGn++++vvselaG+sn++ k+kelG
  lcl|NCBI__GCF_000969705.1:WP_052669621.1 290 LCNQATPDVAPYVGHTAFSHKAGLHASALAKAPDMYQHIEPDDVGNRQRLVVSELAGRSNIVLKAKELG 358
                                               ********************************************************************* PP

                                 TIGR00977 346 ieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalG...krkkyfevdgfrvliakrrdee. 410
                                               +++   + + + +l+++k  e  G+ +eaa+as+ ll+r+  G   +  + f    +rv +     e  
  lcl|NCBI__GCF_000969705.1:WP_052669621.1 359 VDVT--ADQAKAVLAEVKRRESLGWTYEAADASFGLLLRRVAGllaDEDEPFRSLHYRVNVGGGAAEAt 425
                                               8765..567899****************************9772225667899*******987776652 PP

                                 TIGR00977 411 .slseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvriln........ 470
                                                    aea + v v g++ l a eGnGpv+ald+a+r a++  +p+l  ++l dykvril+        
  lcl|NCBI__GCF_000969705.1:WP_052669621.1 426 nGEGPAEAILAVEVAGVRRLGAGEGNGPVDALDHAFRNAVNGTWPDLDRVHLADYKVRILEavsatgdr 494
                                               234457888888899999******************************************843333333 PP

                                 TIGR00977 471 esaGtsaktrvliessdGkrrwgtvGvseniieasytallesie 514
                                               ++ Gt+a trvl+ ++dG  +w tvGv  n++eas+ al ++  
  lcl|NCBI__GCF_000969705.1:WP_052669621.1 495 DGIGTDAVTRVLVTATDGTTKWDTVGVHANVVEASWLALSDAYT 538
                                               4679***********************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (556 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 13.05
//
[ok]

This GapMind analysis is from Apr 10 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