Alignments for a candidate for leuA in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Haloechinothrix alba DSM 45207

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_089301955.1 CHB84_RS13555 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>NCBI__GCF_900188115.1:WP_089301955.1
          Length = 561

 Score =  807 bits (2084), Expect = 0.0
 Identities = 411/604 (68%), Positives = 472/604 (78%), Gaps = 43/604 (7%)

Query: 41  MPVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFD 100
           MP +RYRP+ E VE I L +RTWPD  IDRAPLWCAVDLRDGNQALIDPMSPARKR+ FD
Sbjct: 1   MPYHRYRPWYELVEDITLPDRTWPDVRIDRAPLWCAVDLRDGNQALIDPMSPARKRKFFD 60

Query: 101 LLVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSG 160
           LLV+MGYKEIEVGFP+ASQTDFDFVREII + AIPDDV IQVLTQCR ELIERTFQA  G
Sbjct: 61  LLVQMGYKEIEVGFPAASQTDFDFVREIITEDAIPDDVHIQVLTQCRHELIERTFQALEG 120

Query: 161 APRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESY 220
           A +AIVHFYNSTSI QRRVVFR  R  ++ IAT GA    E AAKY  T +RF+YSPESY
Sbjct: 121 ANKAIVHFYNSTSIAQRRVVFREGREGIKKIATQGAELAKELAAKYTDTSFRFQYSPESY 180

Query: 221 TGTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESV 280
           TGTEL YA ++ +AV E++ PTPE P+I NLPATVEM TPNVYADSIEWM RNL  R+S+
Sbjct: 181 TGTELSYAAEISNAVTEILEPTPEHPVIVNLPATVEMATPNVYADSIEWMGRNLERRDSL 240

Query: 281 ILSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQI 340
           ILSLHPHNDRGTA+AAAELG+ AGADRIEGCLFGNGERTGNV LV LG+NLFS+G+DPQI
Sbjct: 241 ILSLHPHNDRGTAIAAAELGYQAGADRIEGCLFGNGERTGNVDLVALGMNLFSQGIDPQI 300

Query: 341 DFSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCD 400
           DFS+IDEI+RTVEYCNQLPV ER P+GGDLV+TAFSGSHQDAINKG DA++  ADA    
Sbjct: 301 DFSDIDEIKRTVEYCNQLPVGERTPWGGDLVFTAFSGSHQDAINKGFDALEAAADAEGVP 360

Query: 401 VDDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQV 460
           VDD  W+VPYLPIDP+DVGRTYEAVIRVNSQSGKGGVAY+M+++H L LPRRLQ+EFSQV
Sbjct: 361 VDDYPWEVPYLPIDPKDVGRTYEAVIRVNSQSGKGGVAYVMRSEHQLDLPRRLQVEFSQV 420

Query: 461 IQKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKI 520
           +Q+    T  EGGE+ P  MW+AF+ EYL   +PLE +R HV   D+ GG  SIT TV +
Sbjct: 421 VQQY---TDTEGGEIDPTTMWEAFSAEYLTVTQPLELVRSHV--VDNGGGRYSITVTVLV 475

Query: 521 NGVETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIASP 580
           +G E EI+GSGNGP+A+F  AL+ +GFD+ +LDY EHAM+AGDDAQAA+YVE ++     
Sbjct: 476 DGEEQEITGSGNGPIASFFDALSTIGFDIRLLDYSEHAMTAGDDAQAASYVECAI----- 530

Query: 581 AQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSAVN 640
              GE                              +  WGVGI PSI TASLRAV+SAVN
Sbjct: 531 ---GE------------------------------QVYWGVGIDPSIVTASLRAVISAVN 557

Query: 641 RAAR 644
           RA R
Sbjct: 558 RAYR 561


Lambda     K      H
   0.317    0.133    0.399 

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: 997
Number of extensions: 38
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 644
Length of database: 561
Length adjustment: 37
Effective length of query: 607
Effective length of database: 524
Effective search space:   318068
Effective search space used:   318068
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: 53 (25.0 bits)

Align candidate WP_089301955.1 CHB84_RS13555 (2-isopropylmalate synthase)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00970.hmm
# target sequence database:        /tmp/gapView.2280.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00970  [M=564]
Accession:   TIGR00970
Description: leuA_yeast: 2-isopropylmalate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-265  867.3   0.0   2.7e-265  867.2   0.0    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089301955.1  CHB84_RS13555 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089301955.1  CHB84_RS13555 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  867.2   0.0  2.7e-265  2.7e-265       1     564 []       2     561 .]       2     561 .] 0.97

  Alignments for each domain:
  == domain 1  score: 867.2 bits;  conditional E-value: 2.7e-265
                                 TIGR00970   1 pskkykpfk....aiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkei 65 
                                               p ++y+p+      i l++r+wpd +i+rap+w++vdlrdGnqalidpms++rk+++f+llv++G+kei
  lcl|NCBI__GCF_900188115.1:WP_089301955.1   2 PYHRYRPWYelveDITLPDRTWPDVRIDRAPLWCAVDLRDGNQALIDPMSPARKRKFFDLLVQMGYKEI 70 
                                               67899998767779******************************************************* PP

                                 TIGR00970  66 evgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrev 134
                                               evgfp+asqtdfdfvreii + +ipddv iqvltq+r+eli+rt++al+Ga+kaivh+yn+ts+ +r+v
  lcl|NCBI__GCF_900188115.1:WP_089301955.1  71 EVGFPAASQTDFDFVREIITEDAIPDDVHIQVLTQCRHELIERTFQALEGANKAIVHFYNSTSIAQRRV 139
                                               ********************************************************************* PP

                                 TIGR00970 135 vfrasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteer 203
                                               vfr  re + ++a++g++l+++    aak+ +t ++f+yspes+++tel +a e+ +av e++ept+e+
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 140 VFREGREGIKKIATQGAELAKE---LAAKYTDTSFRFQYSPESYTGTELSYAAEISNAVTEILEPTPEH 205
                                               ****************877765...5899**************************************** PP

                                 TIGR00970 204 piifnlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfG 272
                                               p+i nlpatve+atpnvyadsie++ +n+  r+++ilslhphndrGta+aaaelG+ aGadrieGclfG
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 206 PVIVNLPATVEMATPNVYADSIEWMGRNLERRDSLILSLHPHNDRGTAIAAAELGYQAGADRIEGCLFG 274
                                               ********************************************************************* PP

                                 TIGR00970 273 nGertGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdai 341
                                               nGertGnvdlv+l++nl++qG++p++dfsd+dei+r+ve+cn++pv er p+gGdlv+tafsGshqdai
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 275 NGERTGNVDLVALGMNLFSQGIDPQIDFSDIDEIKRTVEYCNQLPVGERTPWGGDLVFTAFSGSHQDAI 343
                                               ********************************************************************* PP

                                 TIGR00970 342 kkGldaldkkkaaa.....dtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprr 405
                                               +kG+dal+  ++a      d  w+vpylp+dpkdvgr+yeavirvnsqsGkGGvayv++ ++ ldlprr
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 344 NKGFDALEAAADAEgvpvdDYPWEVPYLPIDPKDVGRTYEAVIRVNSQSGKGGVAYVMRSEHQLDLPRR 412
                                               ********9999878999999************************************************ PP

                                 TIGR00970 406 lqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikge 474
                                               lq+efs+vv++++d++G+e+++  ++++f  eyl+ +++le ++     v d+G ++ +it +v ++ge
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 413 LQVEFSQVVQQYTDTEGGEIDPTTMWEAFSAEYLTVTQPLELVRS---HVVDNGGGRYSITVTVLVDGE 478
                                               ***********************************7777666655...5667888************** PP

                                 TIGR00970 475 kkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGi 543
                                               +++i GsGnGp++++ dal+ ++ +d+ ++dyseha+++Gdda+aasyve ++ ++        wGvGi
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 479 EQEITGSGNGPIASFFDALSTIG-FDIRLLDYSEHAMTAGDDAQAASYVECAIGEQV------YWGVGI 540
                                               *********************99.**************************9998776......9***** PP

                                 TIGR00970 544 aedvtsaslravlsavnraar 564
                                               ++++ +aslrav+savnra r
  lcl|NCBI__GCF_900188115.1:WP_089301955.1 541 DPSIVTASLRAVISAVNRAYR 561
                                               ******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (561 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: 8.43
//
[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