Alignments for a candidate for cimA in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Haloglycomyces albus DSM 45210

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_025274981.1 HALAL_RS0116090 citramalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000527155.1:WP_025274981.1
          Length = 546

 Score =  429 bits (1104), Expect = e-124
 Identities = 225/523 (43%), Positives = 328/523 (62%), Gaps = 12/523 (2%)

Query: 6   LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE-K 64
           ++DTTLRDG Q E + + V DK+ +A  +DE+G+ YIEGGWPG+ P D  FF+   +E  
Sbjct: 24  IFDTTLRDGAQMEGLRYSVADKMSVARLIDELGVDYIEGGWPGALPSDTEFFERASEEIN 83

Query: 65  LSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLE 124
              AK+ AFG TRRA +    D  L  LI +      +  K+   HV  AL+ S  ENLE
Sbjct: 84  FKHAKLVAFGMTRRAGIAAADDEGLGALIDSRAPTLCLVAKSDIRHVRHALKASPAENLE 143

Query: 125 LIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMP 184
           +I DS+ Y +    EVF D EHFFDG++ +PDYA   +K++ DA AD +VLCDTNGG++P
Sbjct: 144 MIRDSISYGREYDREVFIDCEHFFDGFRHSPDYATTVVKSSFDAGADVVVLCDTNGGSIP 203

Query: 185 FELVEIIREVRKHITAP-------LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGE 237
            ++  II ++R  +          LGIH  ND+ CAVAN+L AV  G++ VQGT NG+GE
Sbjct: 204 SDIARIIGDLRSRLADTMRPEDIRLGIHAQNDTGCAVANTLTAVESGVMHVQGTANGYGE 263

Query: 238 RCGNANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAH 297
           R GNA++ S+I  L+ KM    +    L K+   S  +  +AN+ PN+H  YVG++AFAH
Sbjct: 264 RPGNADIFSVIGGLQTKMGMRVLPPGGLEKMTHTSHSIAAIANMPPNEHAPYVGHAAFAH 323

Query: 298 KGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTL 357
           K G+H SAI+  P  Y H+ P++VGN  R+LV++++GR++I  K+ +  I++  +  V  
Sbjct: 324 KAGLHASAIKTDPGLYNHIDPQVVGNDMRILVTEMAGRASIELKSRDLGIELRGQKDVLD 383

Query: 358 EILENIKEMENRGYQFEGAEASFELLMKRALGTHRKF---FSVIGFRVIDEKRHEDQKPL 414
            + + +K++E +G+ FE A+ASFELL+   L    +    F+V  +RVI +    D   +
Sbjct: 384 RVTKRVKDLEAQGWSFEAADASFELLLDDELPQANRVVRPFTVASYRVIID-HTRDGSVV 442

Query: 415 SEATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQG 474
            EAT+ ++V G+   T A+  GPVNALD ALR+AL + +P L E+ L DYKVR+L    G
Sbjct: 443 CEATVRLEVDGEQTITTAQARGPVNALDAALRQALAERFPGLSEINLSDYKVRILAGTSG 502

Query: 475 TASSIRVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKL 517
           T +  RVL    D +  W TVGV +NIV+AS++AL+D++ Y+L
Sbjct: 503 TEAITRVLTTLSDGDDEWTTVGVDDNIVEASWRALIDALTYRL 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: 694
Number of extensions: 24
Number of successful extensions: 4
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_025274981.1 HALAL_RS0116090 (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.2039627.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-183  595.2   0.0   5.2e-183  595.0   0.0    1.0  1  NCBI__GCF_000527155.1:WP_025274981.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000527155.1:WP_025274981.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.0   0.0  5.2e-183  5.2e-183       3     518 ..      23     546 .]      21     546 .] 0.97

  Alignments for each domain:
  == domain 1  score: 595.0 bits;  conditional E-value: 5.2e-183
                             TIGR00977   3 klydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvk.eenlknakvvafsst 74 
                                           +++dttlrdGaq+eG+ +s+ dk+ +a+ +d+lG++yieGGwpga p d++ffe++  e n+k+ak+vaf+ t
  NCBI__GCF_000527155.1:WP_025274981.1  23 HIFDTTLRDGAQMEGLRYSVADKMSVARLIDELGVDYIEGGWPGALPSDTEFFERASeEINFKHAKLVAFGMT 95 
                                           79***************************************************9886167************* PP

                             TIGR00977  75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147
                                           rr   +  +d+ l ali++ +p + +  ks   hv +alk++ +enl+mi d+++y +++ +ev  d ehffd
  NCBI__GCF_000527155.1:WP_025274981.1  96 RRAGIAAADDEGLGALIDSRAPTLCLVAKSDIRHVRHALKASPAENLEMIRDSISYGREYDREVFIDCEHFFD 168
                                           ************************************************************************* PP

                             TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrl......kdpqlGihahndsetava 214
                                           G++  p+ya  ++k++ +aGad++vl+dtnGG++p +i  i+ +++ rl       d +lGiha nd++ ava
  NCBI__GCF_000527155.1:WP_025274981.1 169 GFRHSPDYATTVVKSSFDAGADVVVLCDTNGGSIPSDIARIIGDLRSRLadtmrpEDIRLGIHAQNDTGCAVA 241
                                           *************************************************9999888999************** PP

                             TIGR00977 215 nsllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaeivnlaldenmp 287
                                           n+l ave+G ++vqGt nG+Ger Gna++ s+i  lq k+g+ v+++  l+k+t++++ +a i n++++e++p
  NCBI__GCF_000527155.1:WP_025274981.1 242 NTLTAVESGVMHVQGTANGYGERPGNADIFSVIGGLQTKMGMRVLPPGGLEKMTHTSHSIAAIANMPPNEHAP 314
                                           ************************************************************************* PP

                             TIGR00977 288 yvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilk 360
                                           yvG+ afahk G+h+sa+k +p  y+hidp++vGn  +i v+e+aG++ +  k ++lGie+  ++  + ++ k
  NCBI__GCF_000527155.1:WP_025274981.1 315 YVGHAAFAHKAGLHASAIKTDPGLYNHIDPQVVGNDMRILVTEMAGRASIELKSRDLGIELRGQKDVLDRVTK 387
                                           ************************************************************************* PP

                             TIGR00977 361 kikelekqGyhfeaaeaslellvrdalGkrkky...fevdgfrvliakrrdeeslseaeatvrvsvegaeelt 430
                                           ++k+le+qG+ feaa+as+ell+ d l + +++   f v ++rv+i+++rd      +eatvr+ v+g +  t
  NCBI__GCF_000527155.1:WP_025274981.1 388 RVKDLEAQGWSFEAADASFELLLDDELPQANRVvrpFTVASYRVIIDHTRDGS--VVCEATVRLEVDGEQTIT 458
                                           **************************988765434499************994..457899************ PP

                             TIGR00977 431 aaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGkrrwgtvGvseniie 503
                                           +a+  Gpv+ald alr+al + +p l +++l dykvril +++Gt+a trvl   sdG+  w+tvGv +ni+e
  NCBI__GCF_000527155.1:WP_025274981.1 459 TAQARGPVNALDAALRQALAERFPGLSEINLSDYKVRILAGTSGTEAITRVLTTLSDGDDEWTTVGVDDNIVE 531
                                           ************************************************************************* PP

                             TIGR00977 504 asytallesieyklr 518
                                           as+ al++++ y+lr
  NCBI__GCF_000527155.1:WP_025274981.1 532 ASWRALIDALTYRLR 546
                                           ************996 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.39
//
[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 2024 update 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 original 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