Alignments for a candidate for cimA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Phaeobacter inhibens BS107

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate GFF1624 PGA1_c16460 2-isopropylmalate synthase/homocitrate synthase-like protein

Query= BRENDA::Q74C76
         (528 letters)



>FitnessBrowser__Phaeo:GFF1624
          Length = 543

 Score =  424 bits (1090), Expect = e-123
 Identities = 243/542 (44%), Positives = 336/542 (61%), Gaps = 31/542 (5%)

Query: 6   LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKEKL 65
           LYDTTLRDG Q + + F   +K++IA  LD +G+ YIEGGWPG+NP D  FF    +   
Sbjct: 8   LYDTTLRDGQQTQGVQFSTTEKVQIATALDGLGVDYIEGGWPGANPTDSGFFDAAPR--- 64

Query: 66  SQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLEL 125
           ++A + AFG T+RA  + + D  L  ++ A      + GK+ D+HV  AL I+LEENL+ 
Sbjct: 65  TRATMTAFGMTKRAGRSAENDDVLAAVLNAGTAAVCLVGKSHDYHVTHALGITLEENLDN 124

Query: 126 IFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMPF 185
           I  S+ +L A   E  +DAEHFFDGYK NPDYA+   +AA +A A  +VLCDTNGGT+P 
Sbjct: 125 IRASIAHLVAQGREALFDAEHFFDGYKDNPDYALAACRAALEAGARWVVLCDTNGGTLPG 184

Query: 186 ELVEIIREVRKHITAPL-----GIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCG 240
           ++  I+ EV   I A L     GIHTHND+E AVA SL AV  G  Q+QGT+NG GERCG
Sbjct: 185 DVGRIVAEV---IAAGLPGDHLGIHTHNDTENAVACSLAAVDAGARQIQGTLNGLGERCG 241

Query: 241 NANLCSIIPALKLKMKREC-----IGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAF 295
           NANL ++IP L LK          +  + L  L  LSR + E+ N  P K  AYVG SAF
Sbjct: 242 NANLTTLIPTLLLKPPYADQFDIGVSHEGLSTLTALSRMLDEILNRVPTKQAAYVGASAF 301

Query: 296 AHKGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPV 355
           AHK G+H SAI + P TYEH+ P LVGN   + +S+ +G+SN+  +  E  +++++ DP 
Sbjct: 302 AHKAGLHASAILKDPSTYEHIDPALVGNARIIPMSNQAGQSNLRRRLSEAGLRVENGDPA 361

Query: 356 TLEILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKR---HEDQK 412
              ILE IK  E  GY ++ A+ASFE+L +  LG    FF V  ++V  E+R   ++   
Sbjct: 362 LARILERIKTREAEGYSYDTAQASFEILAREELGQLPSFFEVKRYKVTVERRKNKYDRMV 421

Query: 413 PLSEATIMVKVGGK--------IEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDY 464
            LSEA ++VKV G+        ++ T ++  GPVNAL  AL K L ++   L +++L+D+
Sbjct: 422 SLSEAVVVVKVDGQKLLSVSESLDETGSD-RGPVNALAKALTKDLGQYSKALDDMRLVDF 480

Query: 465 KVRVLPAGQGTASSIRVLIESGDKES-RWGTVGVSENIVDASYQALLDSVEYKLHKSEEI 523
           KVR+     GT +  RV+I+S D    RW TVGVS NI+DAS++ALLD++ +KL +  + 
Sbjct: 481 KVRITQG--GTEAVTRVIIDSEDGAGRRWSTVGVSANIIDASFEALLDAIRWKLLRDTDA 538

Query: 524 EG 525
            G
Sbjct: 539 GG 540


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: 692
Number of extensions: 30
Number of successful extensions: 7
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: 543
Length adjustment: 35
Effective length of query: 493
Effective length of database: 508
Effective search space:   250444
Effective search space used:   250444
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 GFF1624 PGA1_c16460 (2-isopropylmalate synthase/homocitrate synthase-like protein)
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.27202.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.9e-184  599.1   0.0   3.6e-184  598.8   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1624  PGA1_c16460 2-isopropylmalate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1624  PGA1_c16460 2-isopropylmalate synthase/homocitrate synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.8   0.0  3.6e-184  3.6e-184       2     522 ..       6     537 ..       5     540 .. 0.94

  Alignments for each domain:
  == domain 1  score: 598.8 bits;  conditional E-value: 3.6e-184
                          TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrrp 77 
                                        l+lydttlrdG q++Gv +s ++k++ia +ld lG++yieGGwpganp d  ff ++ +    +a ++af+ t+r 
  lcl|FitnessBrowser__Phaeo:GFF1624   6 LYLYDTTLRDGQQTQGVQFSTTEKVQIATALDGLGVDYIEGGWPGANPTDSGFFDAAPR---TRATMTAFGMTKRA 78 
                                        89****************************************************98755...6899********** PP

                          TIGR00977  78 dkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGykanp 153
                                         +  e+d  l a+++a+t  v + Gks d hv++al  tleenl+ i  ++++l  +++e ++daehffdGyk np
  lcl|FitnessBrowser__Phaeo:GFF1624  79 GRSAENDDVLAAVLNAGTAAVCLVGKSHDYHVTHALGITLEENLDNIRASIAHLVAQGREALFDAEHFFDGYKDNP 154
                                        **************************************************************************** PP

                          TIGR00977 154 eyalktlkvaekaGadwlvladtnGGtlpheieeitkkvk.krlkdpqlGihahndsetavansllaveaGavqvq 228
                                        +yal++ ++a +aGa w+vl+dtnGGtlp+++  i+ +v    l   +lGih+hnd+e ava sl+av aGa+q+q
  lcl|FitnessBrowser__Phaeo:GFF1624 155 DYALAACRAALEAGARWVVLCDTNGGTLPGDVGRIVAEVIaAGLPGDHLGIHTHNDTENAVACSLAAVDAGARQIQ 230
                                        ***********************************9998615689999**************************** PP

                          TIGR00977 229 GtinGlGercGnanlcslipnlqlkl....gldv.iekenlkkltevarlvaeivnlaldenmpyvGesafahkGG 299
                                        Gt+nGlGercGnanl +lip l lk     ++d+ + +e l  lt ++r++ ei n+ +++++ yvG safahk G
  lcl|FitnessBrowser__Phaeo:GFF1624 231 GTLNGLGERCGNANLTTLIPTLLLKPpyadQFDIgVSHEGLSTLTALSRMLDEILNRVPTKQAAYVGASAFAHKAG 306
                                        *************************7222245666899************************************** PP

                          TIGR00977 300 vhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaa 375
                                        +h+sa+ ++p tyehidp lvGn r+i +s++aG+sn+ ++l e G+ +++ +p++ +il++ik  e++Gy +++a
  lcl|FitnessBrowser__Phaeo:GFF1624 307 LHASAILKDPSTYEHIDPALVGNARIIPMSNQAGQSNLRRRLSEAGLRVENGDPALARILERIKTREAEGYSYDTA 382
                                        **************************************************************************** PP

                          TIGR00977 376 easlellvrdalGkrkkyfevdgfrvliakrrdee..slseaeatvrvsvegae.......eltaaeGnGpvsald 442
                                        +as+e+l r+ lG+  ++fev+ ++v++++r+++    +s +ea v v v+g++         ++    Gpv+al 
  lcl|FitnessBrowser__Phaeo:GFF1624 383 QASFEILAREELGQLPSFFEVKRYKVTVERRKNKYdrMVSLSEAVVVVKVDGQKllsvsesLDETGSDRGPVNALA 458
                                        ***************************998877544467777788888888998455554444455568******* PP

                          TIGR00977 443 ralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvseniieasytallesieykl 517
                                        +al k l ++   l d++l+d+kvri   + Gt+a trv+i+s dG  rrw+tvGvs nii+as+ all++i +kl
  lcl|FitnessBrowser__Phaeo:GFF1624 459 KALTKDLGQYSKALDDMRLVDFKVRIT--QGGTEAVTRVIIDSEDGAgRRWSTVGVSANIIDASFEALLDAIRWKL 532
                                        **************************7..579*************9659*************************** PP

                          TIGR00977 518 rkdee 522
                                         +d+ 
  lcl|FitnessBrowser__Phaeo:GFF1624 533 LRDTD 537
                                        99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (543 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 0.02s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 7.18
//
[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