Aligments for a candidate for cimA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Aligments for a candidate for cimA in Desulfovibrio vulgaris Miyazaki F

Align (R)-citramalate synthase (EC 2.3.1.182) (characterized)
to candidate 8499505 DvMF_0275 putative alpha-isopropylmalate/homocitrate synthase family transferase (RefSeq)

Query= BRENDA::Q74C76
         (528 letters)



>FitnessBrowser__Miya:8499505
          Length = 540

 Score =  569 bits (1467), Expect = e-167
 Identities = 291/526 (55%), Positives = 377/526 (71%), Gaps = 8/526 (1%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           ++LYDTTLRDG+Q+EDI+    DK++IA KLDEIGI  IEGGWPGSNP DVAFFK+I   
Sbjct: 5   IQLYDTTLRDGSQSEDINLTAADKLKIALKLDEIGIDRIEGGWPGSNPVDVAFFKEIANY 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            L  A I+AFGST     T D D NL+ + ++   V +IFGK+ + H  EALR+    NL
Sbjct: 65  HLKHAVISAFGSTHHPNFTADSDPNLRAIAESGARVASIFGKSCEVHAAEALRLDAARNL 124

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           E+I DS+ +LK  + EV++DAEHFFDGY+ N  YA+  L+ A +A AD +VLCDTNGGT+
Sbjct: 125 EIIGDSVAFLKGKLAEVYFDAEHFFDGYRHNAAYALSALRRAHEAGADVLVLCDTNGGTL 184

Query: 184 PFELVEIIREVRKHIT-APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNA 242
           P E+  I+ EVR+ +  A +GIH HND E AVANS+ AV  G VQ+QGTING GERCGNA
Sbjct: 185 PHEVARIVTEVREALPGAAVGIHAHNDCELAVANSIAAVQAGAVQIQGTINGVGERCGNA 244

Query: 243 NLCSIIPALKLKMKRE--CIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGG 300
           NLCSIIP L+LK   E  C+ + +L++L  ++ +V E+AN+ P   Q YVG SAFAHKGG
Sbjct: 245 NLCSIIPTLELKFGGEYTCLPEGRLQQLTAVAAYVSEVANIPPFSRQPYVGRSAFAHKGG 304

Query: 301 VHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEIL 360
           VHVSA+ R    YEH+ P++VGN  R+L+++L+GRSNI++ A  F   +D  +PV   +L
Sbjct: 305 VHVSAVNRKSSLYEHISPDVVGNRQRILITELAGRSNIVSLARRFGFHLDKDEPVVKGLL 364

Query: 361 ENIKEMENRGYQFEGAEASFELLMKRALGTH--RKFFSVIGFRVIDEKRHEDQKPLSEAT 418
             +K+  + GY +  AEAS ELL+ R L     R+FF ++ FRV++ K   + +P+SE +
Sbjct: 365 TELKKKASLGYDYAAAEASVELLILRKLARRGVREFFRLLQFRVLETKHDSEGEPVSEVS 424

Query: 419 IMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVL---PAGQGT 475
           +MV V G  EHTAA G GPVNALDNALRKAL  FYPRL E++LLD+KVRVL     G GT
Sbjct: 425 VMVDVEGVTEHTAATGRGPVNALDNALRKALLGFYPRLSEMRLLDFKVRVLTGAETGGGT 484

Query: 476 ASSIRVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSE 521
           AS++RVLIESGD +SRW TVGVS NI++AS+QAL DSV YKL+K E
Sbjct: 485 ASTVRVLIESGDSDSRWVTVGVSFNIIEASWQALADSVTYKLYKDE 530


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: 784
Number of extensions: 29
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: 528
Length of database: 540
Length adjustment: 35
Effective length of query: 493
Effective length of database: 505
Effective search space:   248965
Effective search space used:   248965
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 8499505 DvMF_0275 (putative alpha-isopropylmalate/homocitrate synthase family transferase (RefSeq))
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.20642.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.7e-209  680.6   0.0   6.5e-209  680.4   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499505  DvMF_0275 putative alpha-isoprop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499505  DvMF_0275 putative alpha-isopropylmalate/homocitrate synthase family transferase (R
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  680.4   0.0  6.5e-209  6.5e-209       2     523 ..       5     532 ..       4     535 .. 0.97

  Alignments for each domain:
  == domain 1  score: 680.4 bits;  conditional E-value: 6.5e-209
                         TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrrpd 78 
                                       ++lydttlrdG+q e + l+  dk++ia kld++Gi+ ieGGwpg+np dvaff+++ +  lk+a ++af+st  p+
  lcl|FitnessBrowser__Miya:8499505   5 IQLYDTTLRDGSQSEDINLTAADKLKIALKLDEIGIDRIEGGWPGSNPVDVAFFKEIANYHLKHAVISAFGSTHHPN 81 
                                       89*************************************************************************** PP

                         TIGR00977  79 kkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGykanpey 155
                                          + d++l+a+ +++++v +ifGks ++h  eal+   + nl++i d+v++lk    ev +daehffdGy+ n  y
  lcl|FitnessBrowser__Miya:8499505  82 FTADSDPNLRAIAESGARVASIFGKSCEVHAAEALRLDAARNLEIIGDSVAFLKGKLAEVYFDAEHFFDGYRHNAAY 158
                                       ***************************************************************************** PP

                         TIGR00977 156 alktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllaveaGavqvqGtin 232
                                       al +l+ a++aGad+lvl+dtnGGtlphe+  i+++v++ l  + +Gihahnd e avans++av+aGavq+qGtin
  lcl|FitnessBrowser__Miya:8499505 159 ALSALRRAHEAGADVLVLCDTNGGTLPHEVARIVTEVREALPGAAVGIHAHNDCELAVANSIAAVQAGAVQIQGTIN 235
                                       ***************************************************************************** PP

                         TIGR00977 233 GlGercGnanlcslipnlqlklg..ldviekenlkkltevarlvaeivnlaldenmpyvGesafahkGGvhvsavkr 307
                                       G+GercGnanlcs+ip l lk+g  + ++++ +l++lt va +v+e+ n+++ ++ pyvG+safahkGGvhvsav+r
  lcl|FitnessBrowser__Miya:8499505 236 GVGERCGNANLCSIIPTLELKFGgeYTCLPEGRLQQLTAVAAYVSEVANIPPFSRQPYVGRSAFAHKGGVHVSAVNR 312
                                       *********************965599************************************************** PP

                         TIGR00977 308 npktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvr 384
                                       ++  yehi+p++vGn+++i ++elaG+sn+++ ++ +G+++d+++p v+ +l ++k+    Gy++ aaeas+ell+ 
  lcl|FitnessBrowser__Miya:8499505 313 KSSLYEHISPDVVGNRQRILITELAGRSNIVSLARRFGFHLDKDEPVVKGLLTELKKKASLGYDYAAAEASVELLIL 389
                                       ***************************************************************************** PP

                         TIGR00977 385 dalGkr..kkyfevdgfrvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdl 459
                                       ++l +r  +++f +  frvl +k+ d e  + +e+ v v veg+ e+taa G Gpv+ald+alrkal  fyp+l ++
  lcl|FitnessBrowser__Miya:8499505 390 RKLARRgvREFFRLLQFRVLETKH-DSEGEPVSEVSVMVDVEGVTEHTAATGRGPVNALDNALRKALLGFYPRLSEM 465
                                       *999854489*********97765.66799*********************************************** PP

                         TIGR00977 460 kltdykvrilne...saGtsaktrvliessdGkrrwgtvGvseniieasytallesieyklrkdeee 523
                                       +l+d+kvr+l +   + Gt +++rvlies d + rw tvGvs niieas++al +s+ ykl kde  
  lcl|FitnessBrowser__Miya:8499505 466 RLLDFKVRVLTGaetGGGTASTVRVLIESGDSDSRWVTVGVSFNIIEASWQALADSVTYKLYKDEHA 532
                                       **********75222679**********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (540 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: 10.91
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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