Alignments for a candidate for cimA in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Desulfovibrio gracilis DSM 16080

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_078716957.1 B5D49_RS06945 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_900167125.1:WP_078716957.1
          Length = 539

 Score =  627 bits (1618), Expect = 0.0
 Identities = 310/526 (58%), Positives = 400/526 (76%), Gaps = 5/526 (0%)

Query: 1   MSLVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDI 60
           M  + LYDTTLRDGTQAE+++   EDKIR+A KLDE+G+HYIEGGWPGSNP D  FF++I
Sbjct: 1   MKKISLYDTTLRDGTQAEELNLTTEDKIRVARKLDELGLHYIEGGWPGSNPTDKQFFREI 60

Query: 61  KKEKLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLE 120
           +K +LS A+I AFGST   + + ++D NL +L++AE  V TIFGKTWD H   AL +SLE
Sbjct: 61  RKHRLSTARITAFGSTHYHRTSAEQDPNLASLLEAETPVLTIFGKTWDLHARTALGVSLE 120

Query: 121 ENLELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNG 180
            NLELI  SLE+L+ +V E+F+DAEHFFDGYKANP + +  +K A +A AD +VLCDTNG
Sbjct: 121 RNLELIHASLEHLRPHVDELFFDAEHFFDGYKANPAFTLDCMKTAHEAGADILVLCDTNG 180

Query: 181 GTMPFELVEIIREVRKHIT-APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERC 239
           GT+P E+V+I+ +V+KH+  A LGIHTHNDSE AVAN+L AV  G VQVQGTING+GERC
Sbjct: 181 GTLPHEIVKIMADVQKHLPDAQLGIHTHNDSELAVANALVAVQHGAVQVQGTINGYGERC 240

Query: 240 GNANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299
           GNANLCSIIP L+LKM  +C+G ++L+ LRD + +V E+ANL P   Q +VG +AFAHKG
Sbjct: 241 GNANLCSIIPCLELKMGLDCLGAERLKMLRDTANYVSEVANLRPFLRQPFVGAAAFAHKG 300

Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359
           G+HVSA+ +  ETYEH+RPE VGN  RVL+SDL+G+SNIL KA++    +D  DP    +
Sbjct: 301 GIHVSAVLKDSETYEHIRPESVGNHQRVLLSDLAGKSNILFKAKQCGFDVDRNDPRLEIL 360

Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATI 419
           L++IK  E  GY++  A+ASFELL++  L     +F+   F V+D KR ED+ PLSEAT+
Sbjct: 361 LDDIKAREEMGYEYSVADASFELLLREKLECPDPYFTFHNFFVLDSKREEDELPLSEATV 420

Query: 420 MVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVR----VLPAGQGT 475
           +V V G+  HTAA GNGPVNALD A+RKALE+FYPRLKEV+L D+KVR    VL    GT
Sbjct: 421 IVSVRGERAHTAASGNGPVNALDRAVRKALERFYPRLKEVRLKDFKVRVVSGVLRDTGGT 480

Query: 476 ASSIRVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSE 521
           AS +RVL+ES D ++ W TVGVS NI++AS+QA++DS+ YK+H  E
Sbjct: 481 ASFVRVLVESSDGQNHWTTVGVSHNIIEASWQAVVDSINYKIHLDE 526


Lambda     K      H
   0.317    0.135    0.387 

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: 841
Number of extensions: 34
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: 528
Length of database: 539
Length adjustment: 35
Effective length of query: 493
Effective length of database: 504
Effective search space:   248472
Effective search space used:   248472
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_078716957.1 B5D49_RS06945 (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.30219.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-229  748.0   0.0   2.6e-229  747.8   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078716957.1  B5D49_RS06945 citramalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078716957.1  B5D49_RS06945 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  747.8   0.0  2.6e-229  2.6e-229       1     524 [.       3     529 ..       3     531 .. 0.98

  Alignments for each domain:
  == domain 1  score: 747.8 bits;  conditional E-value: 2.6e-229
                                 TIGR00977   1 slklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvv 69 
                                               ++ lydttlrdG+qae + l+ edkir+a+kld+lG+hyieGGwpg+np d +ff+++++  l  a+++
  lcl|NCBI__GCF_900167125.1:WP_078716957.1   3 KISLYDTTLRDGTQAEELNLTTEDKIRVARKLDELGLHYIEGGWPGSNPTDKQFFREIRKHRLSTARIT 71 
                                               689****************************************************************** PP

                                 TIGR00977  70 afsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadev 138
                                               af+st       e+d++l +l++aetpv+tifGk+wdlh   al  +le nl++i+ ++e+l+ ++de+
  lcl|NCBI__GCF_900167125.1:WP_078716957.1  72 AFGSTHYHRTSAEQDPNLASLLEAETPVLTIFGKTWDLHARTALGVSLERNLELIHASLEHLRPHVDEL 140
                                               ********************************************************************* PP

                                 TIGR00977 139 iydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahn 207
                                                +daehffdGykanp ++l+ +k+a++aGad+lvl+dtnGGtlphei +i+ +v+k+l d+qlGih+hn
  lcl|NCBI__GCF_900167125.1:WP_078716957.1 141 FFDAEHFFDGYKANPAFTLDCMKTAHEAGADILVLCDTNGGTLPHEIVKIMADVQKHLPDAQLGIHTHN 209
                                               ********************************************************************* PP

                                 TIGR00977 208 dsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvae 276
                                               dse avan+l+av+ GavqvqGtinG+GercGnanlcs+ip l lk+gld++  e+lk l ++a++v+e
  lcl|NCBI__GCF_900167125.1:WP_078716957.1 210 DSELAVANALVAVQHGAVQVQGTINGYGERCGNANLCSIIPCLELKMGLDCLGAERLKMLRDTANYVSE 278
                                               ********************************************************************* PP

                                 TIGR00977 277 ivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelG 345
                                               + nl +  + p+vG  afahkGG+hvsav ++++tyehi pe vGn++++ +s+laGksn+l k+k+ G
  lcl|NCBI__GCF_900167125.1:WP_078716957.1 279 VANLRPFLRQPFVGAAAFAHKGGIHVSAVLKDSETYEHIRPESVGNHQRVLLSDLAGKSNILFKAKQCG 347
                                               ********************************************************************* PP

                                 TIGR00977 346 ieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslse 414
                                               +++d+++p++  +l+ ik  e+ Gy++  a+as+ell+r++l    +yf ++ f vl  kr ++  l+ 
  lcl|NCBI__GCF_900167125.1:WP_078716957.1 348 FDVDRNDPRLEILLDDIKAREEMGYEYSVADASFELLLREKLECPDPYFTFHNFFVLDSKREED-ELPL 415
                                               ********************************************************98877766.7999 PP

                                 TIGR00977 415 aeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvriln....esaGtsakt 479
                                               +eatv vsv g + +taa GnGpv+aldra+rkale+fyp+lk+++l d+kvr++     ++ Gt + +
  lcl|NCBI__GCF_900167125.1:WP_078716957.1 416 SEATVIVSVRGERAHTAASGNGPVNALDRAVRKALERFYPRLKEVRLKDFKVRVVSgvlrDTGGTASFV 484
                                               9****************************************************86522216899***** PP

                                 TIGR00977 480 rvliessdGkrrwgtvGvseniieasytallesieyklrkdeeel 524
                                               rvl+essdG+ +w+tvGvs+niieas++a+++si+yk+++de+e 
  lcl|NCBI__GCF_900167125.1:WP_078716957.1 485 RVLVESSDGQNHWTTVGVSHNIIEASWQAVVDSINYKIHLDECEA 529
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (539 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.18
//
[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