Alignments for a candidate for cimA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Desulfovibrio vulgaris Miyazaki F

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate 8499505 DvMF_0275 putative alpha-isopropylmalate/homocitrate synthase family transferase (RefSeq)

Query= reanno::DvH:207383
         (538 letters)



>FitnessBrowser__Miya:8499505
          Length = 540

 Score =  879 bits (2272), Expect = 0.0
 Identities = 438/538 (81%), Positives = 484/538 (89%)

Query: 1   MRRQIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKE 60
           M R+I LYDTTLRDGSQSEDINL   DKLKIAL+LDE+GI  IEGGWPGSNPVDVAFFKE
Sbjct: 1   MTRRIQLYDTTLRDGSQSEDINLTAADKLKIALKLDEIGIDRIEGGWPGSNPVDVAFFKE 60

Query: 61  IRNYNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDG 120
           I NY+LK A ISAFGSTHHP+ TA++DPNL+AIA +    A+IFGKSCE HA EALRLD 
Sbjct: 61  IANYHLKHAVISAFGSTHHPNFTADSDPNLRAIAESGARVASIFGKSCEVHAAEALRLDA 120

Query: 121 RRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTN 180
            RNL+II DS+AFLK ++AEV+FDAEHFFDGYRHNAAYAL  LRRAHEAG DVLVLCDTN
Sbjct: 121 ARNLEIIGDSVAFLKGKLAEVYFDAEHFFDGYRHNAAYALSALRRAHEAGADVLVLCDTN 180

Query: 181 GGTLPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGER 240
           GGTLPHEV  IVT VRE LP A +GIHAHNDCE+AVANSIAAVQAGAVQ+QGT+NGVGER
Sbjct: 181 GGTLPHEVARIVTEVREALPGAAVGIHAHNDCELAVANSIAAVQAGAVQIQGTINGVGER 240

Query: 241 CGNANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFA 300
           CGNANL S+IP LELK  G Y CLPEGRLQQLTAV++YVSEV N+PPFSRQP+VGRSAFA
Sbjct: 241 CGNANLCSIIPTLELKFGGEYTCLPEGRLQQLTAVAAYVSEVANIPPFSRQPYVGRSAFA 300

Query: 301 HKGGVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVV 360
           HKGGVHVSAVNR ++LYEHI+P+ VGN QR+LITELAGRSNIVSLARRFGFHLDKDEPVV
Sbjct: 301 HKGGVHVSAVNRKSSLYEHISPDVVGNRQRILITELAGRSNIVSLARRFGFHLDKDEPVV 360

Query: 361 KGLMNELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQENDLEPM 420
           KGL+ ELKKKASLGYDYAAAEASVELL+LRKLARRGVREFF+L+QFRVLE+K +++ EP+
Sbjct: 361 KGLLTELKKKASLGYDYAAAEASVELLILRKLARRGVREFFRLLQFRVLETKHDSEGEPV 420

Query: 421 SEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTGTET 480
           SE SVMV+VEG+ EHTAATGRGPVNALDNALRKAL  FYPR+ EMRLLDFKVRVLTG ET
Sbjct: 421 SEVSVMVDVEGVTEHTAATGRGPVNALDNALRKALLGFYPRLSEMRLLDFKVRVLTGAET 480

Query: 481 DGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEHVQRGMTD 538
            GGTASTVRVLIESGD+DSRWVTVGVS+NIIEASWQALADS+TYKLYKDEH +R  +D
Sbjct: 481 GGGTASTVRVLIESGDSDSRWVTVGVSFNIIEASWQALADSVTYKLYKDEHARRAGSD 538


Lambda     K      H
   0.318    0.134    0.382 

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: 890
Number of extensions: 26
Number of successful extensions: 1
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: 538
Length of database: 540
Length adjustment: 35
Effective length of query: 503
Effective length of database: 505
Effective search space:   254015
Effective search space used:   254015
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 (21.7 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.21311.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.40
//
[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