Alignments for a candidate for asd in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Herbaspirillum seropedicae SmR1

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate HSERO_RS16495 HSERO_RS16495 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__HerbieS:HSERO_RS16495
          Length = 370

 Score =  521 bits (1343), Expect = e-153
 Identities = 257/368 (69%), Positives = 299/368 (81%), Gaps = 2/368 (0%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60
           MK VGL+GWRGMVGSVLMQRM +E DFD IEPVFF+TSN GG+ P   K    LKDA SI
Sbjct: 1   MKLVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKKETTLKDANSI 60

Query: 61  DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120
           DELK  D+I+T QGGDYT+E+FPKLR AGW GYWIDAASSLRM+DDAVIVLDPVN  VI 
Sbjct: 61  DELKKCDIIITAQGGDYTNEIFPKLRAAGWDGYWIDAASSLRMKDDAVIVLDPVNNNVIK 120

Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180
            AL  G +NYIGGNCT S++LM +GGLF  GLVEW+S+MTYQAASG GA +MRELLK MG
Sbjct: 121 DALAKGVKNYIGGNCTNSILLMGVGGLFKEGLVEWVSSMTYQAASGGGANHMRELLKGMG 180

Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
             +A+VAD+LA P+SAILDIDRKVA+T+R E  PTE FGAPL G LIPWID +L NGQS+
Sbjct: 181 VINAAVADELATPSSAILDIDRKVAKTIR-EDVPTEFFGAPLAGGLIPWIDAQLENGQSK 239

Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300
           EEWK QAE NKIL   +  IPVDG+CVR+GAMRCHS ALTIKL +D+PL +IE +I   N
Sbjct: 240 EEWKGQAEVNKILGN-EQIIPVDGLCVRIGAMRCHSLALTIKLKRDLPLAEIESIIRAGN 298

Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360
            WVK VPN R ++V+ELTPA++TG L + VGR+RKLN G +Y+ AF +GDQLLWGAAEPL
Sbjct: 299 QWVKWVPNDRAITVKELTPASITGGLEIGVGRVRKLNQGPEYISAFVIGDQLLWGAAEPL 358

Query: 361 RRMLRILL 368
           RRMLRI+L
Sbjct: 359 RRMLRIIL 366


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: 513
Number of extensions: 14
Number of successful extensions: 3
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 HSERO_RS16495 HSERO_RS16495 (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.32210.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     4e-212  689.7   0.5   4.6e-212  689.5   0.5    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS16495  HSERO_RS16495 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS16495  HSERO_RS16495 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.5   0.5  4.6e-212  4.6e-212       2     365 ..       3     365 ..       2     366 .. 0.99

  Alignments for each domain:
  == domain 1  score: 689.5 bits;  conditional E-value: 4.6e-212
                                  TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 
                                                 vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g+kaps+ak +++l+da+ id lk++diii
  lcl|FitnessBrowser__HerbieS:HSERO_RS16495   3 LVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKKETTLKDANSIDELKKCDIII 70 
                                                69****************************************************************** PP

                                  TIGR01745  70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137
                                                t qggdyt+ei+pklr+agw+gywidaasslrmkddavi+ldpvn +vikda++kg+++++ggnct+s
  lcl|FitnessBrowser__HerbieS:HSERO_RS16495  71 TAQGGDYTNEIFPKLRAAGWDGYWIDAASSLRMKDDAVIVLDPVNNNVIKDALAKGVKNYIGGNCTNS 138
                                                ******************************************************************** PP

                                  TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtk 205
                                                +llm++gglf+++lvewvs++tyqaasggga+hmrellk+mgv+   v++ela+pssail+i+rkv+k
  lcl|FitnessBrowser__HerbieS:HSERO_RS16495 139 ILLMGVGGLFKEGLVEWVSSMTYQAASGGGANHMRELLKGMGVINAAVADELATPSSAILDIDRKVAK 206
                                                ******************************************************************** PP

                                  TIGR01745 206 lsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrch 273
                                                ++r e++p+e+f++plag+lipwid ql+ngqs+eewkgqae+nkilg +++i+vdglcvriga+rch
  lcl|FitnessBrowser__HerbieS:HSERO_RS16495 207 TIR-EDVPTEFFGAPLAGGLIPWIDAQLENGQSKEEWKGQAEVNKILGNEQIIPVDGLCVRIGAMRCH 273
                                                ***.**************************************************************** PP

                                  TIGR01745 274 sqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeyl 341
                                                s+altiklk+d++l eie+iira+n+wvk+vpn+r it++eltpa++tg+l+i+vgr+rkln g+ey+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16495 274 SLALTIKLKRDLPLAEIESIIRAGNQWVKWVPNDRAITVKELTPASITGGLEIGVGRVRKLNQGPEYI 341
                                                ******************************************************************** PP

                                  TIGR01745 342 saftvgdqllwgaaeplrrmlril 365
                                                saf++gdqllwgaaeplrrmlri+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16495 342 SAFVIGDQLLWGAAEPLRRMLRII 365
                                                **********************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.63
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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