Alignments for a candidate for cimA in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Rhodospirillum centenum SW SW; ATCC 51521

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_012566191.1 RC1_RS04635 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000016185.1:WP_012566191.1
          Length = 547

 Score =  503 bits (1295), Expect = e-147
 Identities = 271/532 (50%), Positives = 352/532 (66%), Gaps = 17/532 (3%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           V LYDTTLRDG Q   + F V DKI IA +LD +GI Y+EGGWPG+NP D AFF      
Sbjct: 7   VYLYDTTLRDGAQTSGVDFGVADKIAIARELDALGIDYVEGGWPGANPTDDAFFA--APP 64

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            L++A   AFG TRR   +   D  L  L+ +      I GK+WDFHV  AL IS  ENL
Sbjct: 65  ALARATFTAFGMTRRPGRSAANDGGLAALLNSGAPAVCIVGKSWDFHVDVALGISRTENL 124

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           ELI DS+  + A   E  +DAEHFFDGY+ NP++A+  ++AA +A A  IVLCDTNGGT+
Sbjct: 125 ELIRDSVAAIVARGREALFDAEHFFDGYRRNPEFALSCVQAAHEAGARWIVLCDTNGGTL 184

Query: 184 PFELVEIIREVRKHITAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNA 242
           P E+  I+ EV + I    LGIH HND+E AVANSL AV  G   +QGT+NG GERCGNA
Sbjct: 185 PHEIERIVAEVARSIPGGRLGIHCHNDTENAVANSLAAVRAGARMIQGTLNGLGERCGNA 244

Query: 243 NLCSIIPALKLKMKREC-IGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGGV 301
           NL S++P L LK+  E  +    L++L  +SR + E  N +PN+H  YVG SAFAHKGG+
Sbjct: 245 NLVSLLPTLMLKLGYETGVARADLKRLVHVSRMLDERMNRAPNRHAPYVGESAFAHKGGL 304

Query: 302 HVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEILE 361
           HVSA+++ P  YEH+ P+LVGN   +LVSD +GRSN+LA+  E  +++D  D    +++E
Sbjct: 305 HVSAVEKDPACYEHIDPDLVGNRRHILVSDQAGRSNVLARLREVGLEVDPGDGRIGQLVE 364

Query: 362 NIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKR---HEDQKPLSEAT 418
            +K  E  GY ++GAEASFELL +RALG    FF ++ FRV+DE+R     +   LSEAT
Sbjct: 365 AVKRREYEGYAYDGAEASFELLARRALGQVPDFFRLVSFRVLDERRWNARNELVTLSEAT 424

Query: 419 IMVKV---------GGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVL 469
           + V+V          G+   T AEGNGPVNALD ALRKAL   YP+L+ ++L+DYKVR+L
Sbjct: 425 VKVEVPPFAQVGTAPGQPVMTVAEGNGPVNALDQALRKALRDVYPQLEGMRLVDYKVRIL 484

Query: 470 PAGQGTASSIRVLIESGDKE-SRWGTVGVSENIVDASYQALLDSVEYKLHKS 520
               GT +  RV+IE+ D+   RW TVGVS NI+DAS+ AL DS+ Y L++S
Sbjct: 485 TPNDGTKAVTRVMIETQDRSGDRWSTVGVSANIIDASFNALFDSITYCLYRS 536


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: 700
Number of extensions: 21
Number of successful extensions: 6
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: 547
Length adjustment: 35
Effective length of query: 493
Effective length of database: 512
Effective search space:   252416
Effective search space used:   252416
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_012566191.1 RC1_RS04635 (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.2256566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-207  676.4   0.0   1.4e-207  676.1   0.0    1.0  1  NCBI__GCF_000016185.1:WP_012566191.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016185.1:WP_012566191.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  676.1   0.0  1.4e-207  1.4e-207       2     520 ..       7     536 ..       6     541 .. 0.96

  Alignments for each domain:
  == domain 1  score: 676.1 bits;  conditional E-value: 1.4e-207
                             TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 
                                           ++lydttlrdGaq+ Gv + + dki ia++ld lGi+y+eGGwpganp d aff +     l +a  +af+ t
  NCBI__GCF_000016185.1:WP_012566191.1   7 VYLYDTTLRDGAQTSGVDFGVADKIAIARELDALGIDYVEGGWPGANPTDDAFFAAP--PALARATFTAFGMT 77 
                                           89****************************************************875..6799********** PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                           rrp +   +d  l al+++++p v i Gkswd+hv  al  +  enl++i d+v+ +   ++e ++daehffd
  NCBI__GCF_000016185.1:WP_012566191.1  78 RRPGRSAANDGGLAALLNSGAPAVCIVGKSWDFHVDVALGISRTENLELIRDSVAAIVARGREALFDAEHFFD 150
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220
                                           Gy+ npe+al  +++a++aGa w+vl+dtnGGtlpheie i+ +v +++   +lGih hnd+e avansl+av
  NCBI__GCF_000016185.1:WP_012566191.1 151 GYRRNPEFALSCVQAAHEAGARWIVLCDTNGGTLPHEIERIVAEVARSIPGGRLGIHCHNDTENAVANSLAAV 223
                                           ************************************************************************* PP

                             TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgldv.iekenlkkltevarlvaeivnlaldenmpyvGes 292
                                           +aGa+++qGt+nGlGercGnanl sl+p l+lklg++  + + +lk+l++v+r++ e +n+a+++++pyvGes
  NCBI__GCF_000016185.1:WP_012566191.1 224 RAGARMIQGTLNGLGERCGNANLVSLLPTLMLKLGYETgVARADLKRLVHVSRMLDERMNRAPNRHAPYVGES 296
                                           ************************************975899******************************* PP

                             TIGR00977 293 afahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikel 365
                                           afahkGG+hvsav+++p  yehidp+lvGn+r+i vs++aG+snvl +l+e+G+e+d+ + ++ ++++ +k  
  NCBI__GCF_000016185.1:WP_012566191.1 297 AFAHKGGLHVSAVEKDPACYEHIDPDLVGNRRHILVSDQAGRSNVLARLREVGLEVDPGDGRIGQLVEAVKRR 369
                                           ************************************************************************* PP

                             TIGR00977 366 ekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee....slseaeatvrvsvegae....... 427
                                           e +Gy +++aeas+ell r+alG++ ++f + +frvl ++r ++     +lsea+++v v+  ++        
  NCBI__GCF_000016185.1:WP_012566191.1 370 EYEGYAYDGAEASFELLARRALGQVPDFFRLVSFRVLDERRWNARnelvTLSEATVKVEVPPFAQVgtapgqp 442
                                           *************************************998766543456777777777776544446677877 PP

                             TIGR00977 428 eltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvse 499
                                           ++t+aeGnGpv+ald+alrkal   yp+l+ ++l+dykvril  + Gt+a trv+ie+ d    rw+tvGvs 
  NCBI__GCF_000016185.1:WP_012566191.1 443 VMTVAEGNGPVNALDQALRKALRDVYPQLEGMRLVDYKVRILTPNDGTKAVTRVMIETQDRSgDRWSTVGVSA 515
                                           **********************************************************9854268******** PP

                             TIGR00977 500 niieasytallesieyklrkd 520
                                           nii+as++al +si y l + 
  NCBI__GCF_000016185.1:WP_012566191.1 516 NIIDASFNALFDSITYCLYRS 536
                                           ****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (547 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 35.91
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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