Alignments for a candidate for cimA in Trichlorobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Trichlorobacter lovleyi SZ

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_012470093.1 GLOV_RS10115 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000020385.1:WP_012470093.1
          Length = 523

 Score =  897 bits (2319), Expect = 0.0
 Identities = 436/523 (83%), Positives = 482/523 (92%)

Query: 1   MSLVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDI 60
           MSLVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDE+G+HYIEGGWPGSNPKDVAFFKDI
Sbjct: 1   MSLVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDELGVHYIEGGWPGSNPKDVAFFKDI 60

Query: 61  KKEKLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLE 120
           KKEKL QAKIAAFGSTRRAK TP  DHN+KTLI AEPDV TIFGKTWDFHV EALRISLE
Sbjct: 61  KKEKLQQAKIAAFGSTRRAKTTPANDHNIKTLIAAEPDVITIFGKTWDFHVREALRISLE 120

Query: 121 ENLELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNG 180
           ENLELI DSL +LK NV EVFYDAEHFFDGYKANP+YAIKTLKAA+DA  DCI+LCDTNG
Sbjct: 121 ENLELINDSLVFLKQNVAEVFYDAEHFFDGYKANPEYAIKTLKAAEDAGVDCIILCDTNG 180

Query: 181 GTMPFELVEIIREVRKHITAPLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCG 240
           G+MP+E+ +II +VRK I  PLGIHTHND ECAVANS+ AV +GIVQVQGTINGFGERCG
Sbjct: 181 GSMPYEVADIIAKVRKQIKTPLGIHTHNDGECAVANSIVAVDQGIVQVQGTINGFGERCG 240

Query: 241 NANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGG 300
           NANLCSIIPA+KLK+K++CI D+QLR LR++S +++ELANLSP+KH AYVG SAFAHKGG
Sbjct: 241 NANLCSIIPAIKLKLKKDCISDEQLRHLREVSNYIFELANLSPDKHLAYVGKSAFAHKGG 300

Query: 301 VHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEIL 360
           VHVSAIQRHPETYEH+RPELVGN TRVLVSDLSG+SNILAKAEEF I +DSKDPVT EIL
Sbjct: 301 VHVSAIQRHPETYEHIRPELVGNSTRVLVSDLSGKSNILAKAEEFQINLDSKDPVTQEIL 360

Query: 361 ENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATIM 420
           E IKEMENRG+QFEGAEASFEL+MK+ALGTH+KFF V+GFRVIDEKR +DQKP SEAT+M
Sbjct: 361 EEIKEMENRGFQFEGAEASFELMMKKALGTHKKFFQVMGFRVIDEKRTDDQKPTSEATVM 420

Query: 421 VKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSIR 480
           +KVGGKIEHTAAEG+GPVNALDNALRKALEKFYP+LKEVKL DYKVRVLPAGQGTASSIR
Sbjct: 421 IKVGGKIEHTAAEGHGPVNALDNALRKALEKFYPKLKEVKLHDYKVRVLPAGQGTASSIR 480

Query: 481 VLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEI 523
           VLIE GDK SRWGTVGVS+NI+DASYQAL+D +++KLH  + +
Sbjct: 481 VLIELGDKISRWGTVGVSDNIIDASYQALIDGIDFKLHHEDSV 523


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: 982
Number of extensions: 10
Number of successful extensions: 1
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: 523
Length adjustment: 35
Effective length of query: 493
Effective length of database: 488
Effective search space:   240584
Effective search space used:   240584
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_012470093.1 GLOV_RS10115 (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.3706194.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-242  790.0   1.5   4.7e-242  789.8   1.5    1.0  1  NCBI__GCF_000020385.1:WP_012470093.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020385.1:WP_012470093.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.8   1.5  4.7e-242  4.7e-242       2     521 ..       4     521 ..       3     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 789.8 bits;  conditional E-value: 4.7e-242
                             TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 
                                           +klydttlrdG+qae +s+ +edkiria+kld+lG+hyieGGwpg+npkdvaff+++k+e+l++ak++af+st
  NCBI__GCF_000020385.1:WP_012470093.1   4 VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDELGVHYIEGGWPGSNPKDVAFFKDIKKEKLQQAKIAAFGST 76 
                                           79*********************************************************************** PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                           rr +    +d+++++li ae  v+tifGk+wd+hv eal+ +leenl++i d++ +lk+ + ev ydaehffd
  NCBI__GCF_000020385.1:WP_012470093.1  77 RRAKTTPANDHNIKTLIAAEPDVITIFGKTWDFHVREALRISLEENLELINDSLVFLKQNVAEVFYDAEHFFD 149
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220
                                           Gykanpeya+ktlk+ae+aG d+++l+dtnGG++p e+ +i+ kv+k++k p lGih+hnd e avans++av
  NCBI__GCF_000020385.1:WP_012470093.1 150 GYKANPEYAIKTLKAAEDAGVDCIILCDTNGGSMPYEVADIIAKVRKQIKTP-LGIHTHNDGECAVANSIVAV 221
                                           ****************************************************.******************** PP

                             TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaeivnlaldenmpyvGesa 293
                                            +G vqvqGtinG+GercGnanlcs+ip ++lkl  d+i +e+l++l ev++++ e+ nl++d+++ yvG+sa
  NCBI__GCF_000020385.1:WP_012470093.1 222 DQGIVQVQGTINGFGERCGNANLCSIIPAIKLKLKKDCISDEQLRHLREVSNYIFELANLSPDKHLAYVGKSA 294
                                           ************************************************************************* PP

                             TIGR00977 294 fahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikele 366
                                           fahkGGvhvsa++r+p+tyehi pelvGn  ++ vs+l+Gksn+l k++e+ i++d k+p  ++il++ike+e
  NCBI__GCF_000020385.1:WP_012470093.1 295 FAHKGGVHVSAIQRHPETYEHIRPELVGNSTRVLVSDLSGKSNILAKAEEFQINLDSKDPVTQEILEEIKEME 367
                                           ************************************************************************* PP

                             TIGR00977 367 kqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvs 439
                                           ++G++fe+aeas+el++++alG+ kk+f+v gfrv+ +kr+d+   +++eatv + v g+ e+taaeG+Gpv+
  NCBI__GCF_000020385.1:WP_012470093.1 368 NRGFQFEGAEASFELMMKKALGTHKKFFQVMGFRVIDEKRTDD-QKPTSEATVMIKVGGKIEHTAAEGHGPVN 439
                                           ***********************************99999999.889************************** PP

                             TIGR00977 440 aldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGkrrwgtvGvseniieasytalles 512
                                           ald+alrkalekfyp+lk++kl dykvr+l  + Gt + +rvlie  d   rwgtvGvs+nii+asy+al+++
  NCBI__GCF_000020385.1:WP_012470093.1 440 ALDNALRKALEKFYPKLKEVKLHDYKVRVLPAGQGTASSIRVLIELGDKISRWGTVGVSDNIIDASYQALIDG 512
                                           ************************************************************************* PP

                             TIGR00977 513 ieyklrkde 521
                                           i++kl++++
  NCBI__GCF_000020385.1:WP_012470093.1 513 IDFKLHHED 521
                                           *****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (523 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 31.01
//
[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