Alignments for a candidate for cimA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Magnetospirillum magneticum AMB-1

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_011384529.1 AMB_RS10755 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000009985.1:WP_011384529.1
          Length = 546

 Score =  491 bits (1263), Expect = e-143
 Identities = 266/543 (48%), Positives = 357/543 (65%), Gaps = 26/543 (4%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           V LYDTTLRDG Q + + F   DK+RIA +LD IGI Y+EGGWPG+NP D AFF D    
Sbjct: 5   VYLYDTTLRDGAQTQGVDFSAADKVRIARELDRIGIDYVEGGWPGANPTDDAFFADPPAF 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
           K S  ++ AFG TRRA  + D D  L  L+     V T+ GK+WDF V  AL I L+ENL
Sbjct: 65  KRS--RLTAFGMTRRAGRSADNDPGLNALLVTPARVATMVGKSWDFQVTVALGIELDENL 122

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
            ++ DS+++ +  V EV +DAEHFFDGYKANP YA+   KAA DA A  +VLCDTNGGT+
Sbjct: 123 RMVADSVQHARTKVEEVMFDAEHFFDGYKANPAYALAAAKAAYDAGARWVVLCDTNGGTL 182

Query: 184 PFELVEIIREVRKH--ITAPLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGN 241
           P E+  I+ EV K     + LG+H HNDS+ AVANSL AV  G+ Q+QGT+NG GERCGN
Sbjct: 183 PHEMRRIVGEVIKGGIPGSHLGVHCHNDSDTAVANSLAAVEAGVRQIQGTLNGLGERCGN 242

Query: 242 ANLCSIIPALKLKMKREC-IGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGG 300
           ANL SIIPAL LKM  +  I  + L+ L  +SR + E+ + +PN+ Q YVG SAFAHKGG
Sbjct: 243 ANLISIIPALMLKMGFDTGIAPEDLKNLVSVSRALDEVLDRTPNRGQPYVGKSAFAHKGG 302

Query: 301 VHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTL--- 357
           +HVSA+ + P+ YEH+ P  VGNM  +++SD +GRSN++A+  E  I +DS    +L   
Sbjct: 303 LHVSAVAKDPKCYEHVDPASVGNMRHIVMSDQAGRSNLVARLTEIGIDLDSVKRESLVRV 362

Query: 358 --------------EILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVI 403
                         ++++ +K +E+ GY ++ A ASFELL++RALG   ++F++  +RVI
Sbjct: 363 VDQMQVTFDAREATDLVDLVKRLEHEGYAYDQAAASFELLVRRALGEVPEYFALERYRVI 422

Query: 404 DEKR---HEDQKPLSEATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVK 460
           DE+R   H +   LSEAT+ V+VGG       EG GPV+A D ALRK L + YP L  ++
Sbjct: 423 DERRRNAHGEWITLSEATVKVEVGGTEYMEVGEGTGPVHAFDVALRKVLTRVYPALTALE 482

Query: 461 LLDYKVRVLPAGQGTASSIRVLIES-GDKESRWGTVGVSENIVDASYQALLDSVEYKLHK 519
           L DY+VR+  +  GTA+  RV IES  DK  RW TVGV  N+++AS +AL DS+ + L +
Sbjct: 483 LKDYRVRITESTVGTAAKTRVTIESEDDKGHRWTTVGVHTNVLEASLEALQDSITFMLFR 542

Query: 520 SEE 522
            ++
Sbjct: 543 FKD 545


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: 689
Number of extensions: 23
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: 546
Length adjustment: 35
Effective length of query: 493
Effective length of database: 511
Effective search space:   251923
Effective search space used:   251923
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 WP_011384529.1 AMB_RS10755 (citramalate synthase)
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.21928.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-199  649.8   0.2   9.5e-199  646.9   0.2    1.9  1  lcl|NCBI__GCF_000009985.1:WP_011384529.1  AMB_RS10755 citramalate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384529.1  AMB_RS10755 citramalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.9   0.2  9.5e-199  9.5e-199       2     519 ..       5     542 ..       4     546 .] 0.94

  Alignments for each domain:
  == domain 1  score: 646.9 bits;  conditional E-value: 9.5e-199
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               ++lydttlrdGaq++Gv +s  dk+ria++ld +Gi+y+eGGwpganp d aff +     +k+ +++a
  lcl|NCBI__GCF_000009985.1:WP_011384529.1   5 VYLYDTTLRDGAQTQGVDFSAADKVRIARELDRIGIDYVEGGWPGANPTDDAFFAD--PPAFKRSRLTA 71 
                                               89****************************************************75..678******** PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+ trr  +  ++d+ l+al+ + ++v t+ Gkswd+ v+ al   l+enl+m+ d+v++ +  ++ev+
  lcl|NCBI__GCF_000009985.1:WP_011384529.1  72 FGMTRRAGRSADNDPGLNALLVTPARVATMVGKSWDFQVTVALGIELDENLRMVADSVQHARTKVEEVM 140
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkv.kkrlkdpqlGihahn 207
                                               +daehffdGykanp yal++ k+a +aGa w+vl+dtnGGtlphe+  i+ +v k  +  ++lG+h hn
  lcl|NCBI__GCF_000009985.1:WP_011384529.1 141 FDAEHFFDGYKANPAYALAAAKAAYDAGARWVVLCDTNGGTLPHEMRRIVGEViKGGIPGSHLGVHCHN 209
                                               **************************************************8873667999********* PP

                                 TIGR00977 208 dsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldv.iekenlkkltevarlva 275
                                               ds+tavansl+aveaG +q+qGt+nGlGercGnanl s+ip l+lk+g+d  i +e+lk+l++v+r + 
  lcl|NCBI__GCF_000009985.1:WP_011384529.1 210 DSDTAVANSLAAVEAGVRQIQGTLNGLGERCGNANLISIIPALMLKMGFDTgIAPEDLKNLVSVSRALD 278
                                               **************************************************769**************** PP

                                 TIGR00977 276 eivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkel 344
                                               e+ ++++++  pyvG+safahkGG+hvsav ++pk yeh+dp  vGn r+iv+s++aG+sn++ +l e+
  lcl|NCBI__GCF_000009985.1:WP_011384529.1 279 EVLDRTPNRGQPYVGKSAFAHKGGLHVSAVAKDPKCYEHVDPASVGNMRHIVMSDQAGRSNLVARLTEI 347
                                               ********************************************************************* PP

                                 TIGR00977 345 Gieideks.................pkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfev 396
                                               Gi++d  +                  +  ++++ +k le++Gy ++ a as+ellvr+alG++ +yf +
  lcl|NCBI__GCF_000009985.1:WP_011384529.1 348 GIDLDSVKreslvrvvdqmqvtfdaREATDLVDLVKRLEHEGYAYDQAAASFELLVRRALGEVPEYFAL 416
                                               ****964311111111111111111234568999*********************************** PP

                                 TIGR00977 397 dgfrvliakrrdee..slseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltd 463
                                               + +rv+ ++rr++    ++ +eatv+v v g+e +++ eG Gpv+a+d alrk l++ yp l  l+l d
  lcl|NCBI__GCF_000009985.1:WP_011384529.1 417 ERYRVIDERRRNAHgeWITLSEATVKVEVGGTEYMEVGEGTGPVHAFDVALRKVLTRVYPALTALELKD 485
                                               *******99999865478889************************************************ PP

                                 TIGR00977 464 ykvrilnesaGtsaktrvliessdGk.rrwgtvGvseniieasytallesieyklrk 519
                                               y+vri + + Gt aktrv ies d k  rw+tvGv  n++eas  al++si + l +
  lcl|NCBI__GCF_000009985.1:WP_011384529.1 486 YRVRITESTVGTAAKTRVTIESEDDKgHRWTTVGVHTNVLEASLEALQDSITFMLFR 542
                                               **********************9987479***********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (546 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 3.24
//
[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