Alignments for a candidate for cimA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Dinoroseobacter shibae DFL-12

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate 3608293 Dshi_1696 2-isopropylmalate synthase/homocitrate synthase family protein (RefSeq)

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



>FitnessBrowser__Dino:3608293
          Length = 545

 Score =  414 bits (1065), Expect = e-120
 Identities = 240/544 (44%), Positives = 335/544 (61%), Gaps = 24/544 (4%)

Query: 1   MRRQIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKE 60
           M  +++LYDTTLRDG Q++ +  +TP+K +IA  LD LGI +IEGGWPG+NP D  FF  
Sbjct: 1   MNERLYLYDTTLRDGQQTQGVQFSTPEKQQIAAALDALGIDFIEGGWPGANPTDSEFFAS 60

Query: 61  IRNYNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDG 120
              ++   A+ +AFG T     +AEND  L A+  A T A  + GKS E H   AL +  
Sbjct: 61  APTFD--HARFAAFGMTKRAGFSAENDDVLAAVLNAGTQAVCLVGKSHEYHVTRALGISL 118

Query: 121 RRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTN 180
             N + I  S+A L  Q  E  FDAEHFFDGY  N  YA+E L+ A EAG   +VLCDTN
Sbjct: 119 AENTENIARSVAHLVAQGREAIFDAEHFFDGYLANPGYAVETLQAALEAGARWVVLCDTN 178

Query: 181 GGTLPHEVHDIVT-AVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGE 239
           GG LP EV  I    +   +P  +LGIH HND   AVAN++AA+ AGA QVQGT+NG+GE
Sbjct: 179 GGRLPAEVGRITAEVIAAGVPGDRLGIHTHNDTGNAVANALAAIDAGARQVQGTLNGLGE 238

Query: 240 RCGNANLSSVIPILELKSAGA---YACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGR 296
           RCGNANL ++IP L LK   A      +    L+ L  VS  + ++ N  P    P+VG 
Sbjct: 239 RCGNANLVTLIPTLLLKEPYASRFETGVSAAALRDLVRVSRTLDDILNRVPTKSAPYVGA 298

Query: 297 SAFAHKGGVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKD 356
           SAFAHK G+H SA+ ++ + YEHI PE+VGN + + ++  AG+SN+       G  + K 
Sbjct: 299 SAFAHKAGLHASAILKDPSTYEHIPPEAVGNARVIPMSNQAGQSNLRKRLADAGIAVQKG 358

Query: 357 EPVVKGLMNELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQEND 416
           +  +  L++E+K++  +GY + +A+AS ELL  R L   G+ EFF++ ++RV   +++N 
Sbjct: 359 DMRLGALLDEVKRREDMGYSFDSAQASFELLARRHL--EGLPEFFEVKRYRVTVERRKNK 416

Query: 417 LEPM---SEASVMVEVE-----GIIEHTAATG--RGPVNALDNALRKALSSFYPRIREMR 466
            + M   SEA V++++       + E    TG  RGPVNAL  AL K L  + P I ++R
Sbjct: 417 YDRMVSLSEAVVVLKIGDEKMLSVSESMDETGCDRGPVNALAKALGKDLGPYTPYIADLR 476

Query: 467 LLDFKVRVLTGTETDGGTASTVRVLIESGDADS-RWVTVGVSYNIIEASWQALADSMTYK 525
           L+DFKVR+     T+GGT +  RVLI+S D    RW TVGVS NI++AS++AL +++ +K
Sbjct: 477 LVDFKVRI-----TNGGTEAVTRVLIDSEDGQGRRWSTVGVSANIVDASFEALVEAIQWK 531

Query: 526 LYKD 529
           L +D
Sbjct: 532 LIRD 535


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: 649
Number of extensions: 28
Number of successful extensions: 8
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: 545
Length adjustment: 35
Effective length of query: 503
Effective length of database: 510
Effective search space:   256530
Effective search space used:   256530
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 3608293 Dshi_1696 (2-isopropylmalate synthase/homocitrate synthase family protein (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.10537.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.7e-177  574.8   0.0   8.2e-177  574.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608293  Dshi_1696 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608293  Dshi_1696 2-isopropylmalate synthase/homocitrate synthase family protein (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.5   0.0  8.2e-177  8.2e-177       2     520 ..       5     535 ..       4     540 .. 0.95

  Alignments for each domain:
  == domain 1  score: 574.5 bits;  conditional E-value: 8.2e-177
                         TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrrpd 78 
                                       l+lydttlrdG q++Gv +s  +k +ia +ld lGi++ieGGwpganp d +ff  +    +++a+ +af+ t+r  
  lcl|FitnessBrowser__Dino:3608293   5 LYLYDTTLRDGQQTQGVQFSTPEKQQIAAALDALGIDFIEGGWPGANPTDSEFFASA--PTFDHARFAAFGMTKRAG 79 
                                       89****************************************************876..5799************** PP

                         TIGR00977  79 kkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGykanpey 155
                                          e+d  l a+++a+t+ v + Gks + hv+ al  +l+en + i  +v++l  +++e i+daehffdGy anp y
  lcl|FitnessBrowser__Dino:3608293  80 FSAENDDVLAAVLNAGTQAVCLVGKSHEYHVTRALGISLAENTENIARSVAHLVAQGREAIFDAEHFFDGYLANPGY 156
                                       ***************************************************************************** PP

                         TIGR00977 156 alktlkvaekaGadwlvladtnGGtlpheieeitkkvkk.rlkdpqlGihahndsetavansllaveaGavqvqGti 231
                                       a++tl++a +aGa w+vl+dtnGG lp e+  it +v    +   +lGih+hnd++ avan+l+a+ aGa+qvqGt+
  lcl|FitnessBrowser__Dino:3608293 157 AVETLQAALEAGARWVVLCDTNGGRLPAEVGRITAEVIAaGVPGDRLGIHTHNDTGNAVANALAAIDAGARQVQGTL 233
                                       **********************************998651689999******************************* PP

                         TIGR00977 232 nGlGercGnanlcslipnlqlklgldv.....iekenlkkltevarlvaeivnlaldenmpyvGesafahkGGvhvs 303
                                       nGlGercGnanl +lip l lk  +       +    l+ l+ v+r + +i n+ +++ +pyvG safahk G+h+s
  lcl|FitnessBrowser__Dino:3608293 234 NGLGERCGNANLVTLIPTLLLKEPYASrfetgVSAAALRDLVRVSRTLDDILNRVPTKSAPYVGASAFAHKAGLHAS 310
                                       **********************987542222478899**************************************** PP

                         TIGR00977 304 avkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaaeasle 380
                                       a+ ++p tyehi pe vGn r i +s++aG+sn+ ++l + Gi++++ + ++  +l+++k  e+ Gy f++a+as+e
  lcl|FitnessBrowser__Dino:3608293 311 AILKDPSTYEHIPPEAVGNARVIPMSNQAGQSNLRKRLADAGIAVQKGDMRLGALLDEVKRREDMGYSFDSAQASFE 387
                                       ***************************************************************************** PP

                         TIGR00977 381 llvrdalGkrkkyfevdgfrvliakrrdee....slseaeatvrvsvegae.....eltaaeGnGpvsaldralrka 448
                                       ll r++l    ++fev+ +rv++++r+++     slsea + +++ +e +      + ++    Gpv+al +al k 
  lcl|FitnessBrowser__Dino:3608293 388 LLARRHLEGLPEFFEVKRYRVTVERRKNKYdrmvSLSEAVVVLKIGDEKMLsvsesMDETGCDRGPVNALAKALGKD 464
                                       ***********************99887655678999999999999997654444455666779************* PP

                         TIGR00977 449 lekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvseniieasytallesieyklrkd 520
                                       l  + p ++dl+l+d+kvri n+  Gt+a trvli+s dG+ rrw+tvGvs ni++as+ al+e+i++kl +d
  lcl|FitnessBrowser__Dino:3608293 465 LGPYTPYIADLRLVDFKVRITNG--GTEAVTRVLIDSEDGQgRRWSTVGVSANIVDASFEALVEAIQWKLIRD 535
                                       ********************986..9**************779***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (545 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.51
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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