Alignments for a candidate for asd in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Pseudomonas stutzeri RCH2

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate GFF2538 Psest_2588 aspartate-semialdehyde dehydrogenase, gamma-proteobacterial

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__psRCH2:GFF2538
          Length = 370

 Score =  683 bits (1763), Expect = 0.0
 Identities = 336/370 (90%), Positives = 356/370 (96%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60
           MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGP++GK+ A LKDAYSI
Sbjct: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPDIGKETAALKDAYSI 60

Query: 61  DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120
           DELK LDVILTCQGGDYT+EVFPKLREAGWQGYWIDAASSLRM+DDAVIVLDPVNR+VID
Sbjct: 61  DELKGLDVILTCQGGDYTNEVFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRRVID 120

Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180
           Q LDAGT+NYIGGNCTVSL LM LGGLF+AGLVEWMSAMTYQAASGAGAQNMREL+KQMG
Sbjct: 121 QQLDAGTKNYIGGNCTVSLALMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMG 180

Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
           A +A+VADDLANPASAILDIDRKVAET RSEAFP ++FG PL GSLIP+IDKELPNGQSR
Sbjct: 181 AINAAVADDLANPASAILDIDRKVAETQRSEAFPVDNFGVPLAGSLIPYIDKELPNGQSR 240

Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300
           EEWKAQAETNKIL RFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVP++DIEGLISQHN
Sbjct: 241 EEWKAQAETNKILGRFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPISDIEGLISQHN 300

Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360
           PWVKLVPNHR+ S++EL+PAAVTGTLSVPVGRLRKLNMGS YLGAFTVGDQLLWGAAEPL
Sbjct: 301 PWVKLVPNHRDASMQELSPAAVTGTLSVPVGRLRKLNMGSHYLGAFTVGDQLLWGAAEPL 360

Query: 361 RRMLRILLER 370
           RRMLRILLER
Sbjct: 361 RRMLRILLER 370


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: 634
Number of extensions: 14
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: 370
Length of database: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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 GFF2538 Psest_2588 (aspartate-semialdehyde dehydrogenase, gamma-proteobacterial)
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.3668066.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.8e-200  649.1   0.0     1e-199  648.9   0.0    1.0  1  FitnessBrowser__psRCH2:GFF2538  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__psRCH2:GFF2538  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.9   0.0    1e-199    1e-199       1     366 []       2     368 ..       2     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 648.9 bits;  conditional E-value: 1e-199
                       TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqggdytke 79 
                                     k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++p ++k +a+l+day id lk ld+i+tcqggdyt+e
  FitnessBrowser__psRCH2:GFF2538   2 KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPDIGKETAALKDAYSIDELKGLDVILTCQGGDYTNE 80 
                                     68***************************************************************************** PP

                       TIGR01745  80 iypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrdelvewvsva 158
                                     ++pklr+agw+gywidaasslrm+ddavi+ldpvn  vi++ ++ g+++++ggnctvsl lm+lgglf+ +lvew+s++
  FitnessBrowser__psRCH2:GFF2538  81 VFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRRVIDQQLDAGTKNYIGGNCTVSLALMGLGGLFEAGLVEWMSAM 159
                                     ******************************************************************************* PP

                       TIGR01745 159 tyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplagslipwidkqldngq 237
                                     tyqaasg+ga+ mrel+kqmg +   v+++la+p+sail+i+rkv+++ rse +pv+nf+vplagslip+idk+l ngq
  FitnessBrowser__psRCH2:GFF2538 160 TYQAASGAGAQNMRELIKQMGAINAAVADDLANPASAILDIDRKVAETQRSEAFPVDNFGVPLAGSLIPYIDKELPNGQ 238
                                     ******************************************************************************* PP

                       TIGR01745 238 sreewkgqaetnkilgt.kdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlrel 315
                                     sreewk qaetnkilg  k+ i+vdg+cvr+ga+rchsqaltikl+kdv++ +ie +i +hn+wvk+vpn+r+ +++el
  FitnessBrowser__psRCH2:GFF2538 239 SREEWKAQAETNKILGRfKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPISDIEGLISQHNPWVKLVPNHRDASMQEL 317
                                     ***************964789********************************************************** PP

                       TIGR01745 316 tpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366
                                     +paavtgtl++pvgrlrklnmg +yl aftvgdqllwgaaeplrrmlrill
  FitnessBrowser__psRCH2:GFF2538 318 SPAAVTGTLSVPVGRLRKLNMGSHYLGAFTVGDQLLWGAAEPLRRMLRILL 368
                                     *************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (370 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: 15.15
//
[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