GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Klebsiella michiganensis M5al

Align aspartate-semialdehyde dehydrogenase (characterized)
to candidate BWI76_RS26220 BWI76_RS26220 aspartate-semialdehyde dehydrogenase

Query= CharProtDB::CH_024631
         (367 letters)



>FitnessBrowser__Koxy:BWI76_RS26220
          Length = 368

 Score =  687 bits (1772), Expect = 0.0
 Identities = 343/368 (93%), Positives = 357/368 (97%), Gaps = 1/368 (0%)

Query: 1   MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTG-TLQDAFD 59
           MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQ APSFGG+TG TLQDAFD
Sbjct: 1   MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQPAPSFGGSTGGTLQDAFD 60

Query: 60  LEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVI 119
           LEALKALDIIVTCQGGDYTN+IYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVI
Sbjct: 61  LEALKALDIIVTCQGGDYTNDIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVI 120

Query: 120 TDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQM 179
           T GLNNG++TFVGGNCTVSLMLMSLGGLFA DLV+WVSVATYQAASGGGARHMRELLTQM
Sbjct: 121 TAGLNNGVKTFVGGNCTVSLMLMSLGGLFAQDLVEWVSVATYQAASGGGARHMRELLTQM 180

Query: 180 GHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQS 239
           G L+ HVA ELA P+SAIL+IERKVT+LTRSGEL VDNFGVPLAGSLIPWIDKQLDNGQS
Sbjct: 181 GQLHSHVAAELADPASAILEIERKVTSLTRSGELAVDNFGVPLAGSLIPWIDKQLDNGQS 240

Query: 240 REEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHN 299
           REEWKGQAETNKIL T+S IPVDGLCVRVGALRCHSQAFTIKLKK+VSIPTVEELLAAHN
Sbjct: 241 REEWKGQAETNKILATASPIPVDGLCVRVGALRCHSQAFTIKLKKEVSIPTVEELLAAHN 300

Query: 300 PWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPL 359
           PWAKVVPNDR+ITMRELTPAAVTGTLTTPVGRLRKLNMGPE+LSAFTVGDQLLWGAAEPL
Sbjct: 301 PWAKVVPNDRDITMRELTPAAVTGTLTTPVGRLRKLNMGPEYLSAFTVGDQLLWGAAEPL 360

Query: 360 RRMLRQLA 367
           RRML+QLA
Sbjct: 361 RRMLKQLA 368


Lambda     K      H
   0.319    0.136    0.409 

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: 582
Number of extensions: 14
Number of successful extensions: 2
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: 367
Length of database: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS26220 BWI76_RS26220 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR01745.hmm
# target sequence database:        /tmp/gapView.3512839.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01745  [M=366]
Accession:   TIGR01745
Description: asd_gamma: aspartate-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.9e-222  722.4   0.0   5.5e-222  722.2   0.0    1.0  1  FitnessBrowser__Koxy:BWI76_RS26220  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Koxy:BWI76_RS26220  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.2   0.0  5.5e-222  5.5e-222       1     365 [.       2     367 ..       2     368 .] 0.99

  Alignments for each domain:
  == domain 1  score: 722.2 bits;  conditional E-value: 5.5e-222
                           TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa.iledaydidalkeldiiitcqgg 74 
                                         k+vg++gwrgmvgsvl++rm+ee+dfdai+pvffstsqlgq aps+++ ++ +l+da+d++alk+ldii+tcqgg
  FitnessBrowser__Koxy:BWI76_RS26220   2 KNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQPAPSFGGSTGgTLQDAFDLEALKALDIIVTCQGG 76 
                                         69********************************************998877*********************** PP

                           TIGR01745  75 dytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrd 149
                                         dyt++iypklr++gw+gywidaasslrmkdda+iildpvn+dvi+ ++n+g++tfvggnctvsl+lmslgglf++
  FitnessBrowser__Koxy:BWI76_RS26220  77 DYTNDIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITAGLNNGVKTFVGGNCTVSLMLMSLGGLFAQ 151
                                         *************************************************************************** PP

                           TIGR01745 150 elvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplags 224
                                         +lvewvsvatyqaasgggarhmrell+qmg l+ +v+ ela p+saileierkvt l+rs+el v+nf+vplags
  FitnessBrowser__Koxy:BWI76_RS26220 152 DLVEWVSVATYQAASGGGARHMRELLTQMGQLHSHVAAELADPASAILEIERKVTSLTRSGELAVDNFGVPLAGS 226
                                         *************************************************************************** PP

                           TIGR01745 225 lipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnk 299
                                         lipwidkqldngqsreewkgqaetnkil+t++ i+vdglcvr+galrchsqa+tiklkk+vs++++ee+++ahn+
  FitnessBrowser__Koxy:BWI76_RS26220 227 LIPWIDKQLDNGQSREEWKGQAETNKILATASPIPVDGLCVRVGALRCHSQAFTIKLKKEVSIPTVEELLAAHNP 301
                                         *************************************************************************** PP

                           TIGR01745 300 wvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365
                                         w+kvvpn+r+it+reltpaavtgtl++pvgrlrklnmg+eylsaftvgdqllwgaaeplrrml++l
  FitnessBrowser__Koxy:BWI76_RS26220 302 WAKVVPNDRDITMRELTPAAVTGTLTTPVGRLRKLNMGPEYLSAFTVGDQLLWGAAEPLRRMLKQL 367
                                         ****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (368 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.03
//
[ok]

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

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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:

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:

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:

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:

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