Alignments for a candidate for asd in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Klebsiella michiganensis M5al

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate BWI76_RS12880 BWI76_RS12880 aspartate-semialdehyde dehydrogenase

Query= BRENDA::C5BB06
         (367 letters)



>FitnessBrowser__Koxy:BWI76_RS12880
          Length = 372

 Score =  420 bits (1079), Expect = e-122
 Identities = 208/369 (56%), Positives = 265/369 (71%), Gaps = 4/369 (1%)

Query: 1   MKNVGFIGWRGMVGSVLMQRMSEERDFDAIRPLFFSTSQHGQPAPTFGGHGGTLQDASDI 60
           MK VG +GWRGMVGSVL+QRM EE DFD I   FFSTS  G   P   G   TL+DA+ +
Sbjct: 1   MKQVGIVGWRGMVGSVLLQRMIEENDFDNISAHFFSTSSAGAAGPVIDGISYTLKDANSV 60

Query: 61  DALKALDIIITCQGGDYTHAVYPRLRAAGWQGYWIDAASALRMQDDAIIILDPVNRAVID 120
            AL  +DIIITCQGGDYT A+YP L   GW GYWIDAASALRM + A IILDPVNR  ID
Sbjct: 61  SALAEMDIIITCQGGDYTKAIYPNLLNHGWGGYWIDAASALRMDEKACIILDPVNRNNID 120

Query: 121 RGLENGVKTFVGGNCTVSLMLMSLGGLFAADLVEWVSVATYQAASGGGARHMRELLTQMG 180
           R ++ G+K FVGGNC+++L LM L GL  ADL+EW+SV TYQ+ASG GA+++REL+ Q  
Sbjct: 121 RAIKEGIKLFVGGNCSITLSLMGLAGLIKADLIEWMSVMTYQSASGAGAQYVRELIAQSA 180

Query: 181 MLHGQVAPALENPASAILDIERQVTDLMRNGTLPTDNFGVPLAGSLIPWIDKALDNGQSR 240
            +   ++P     + ++L +  +V++L+ +  +PT NFG PL GS+IPWID  L +G SR
Sbjct: 181 YISRHLSPDELASSGSVLPLVNKVSELINSADMPTQNFGAPLMGSIIPWIDSDLGDGNSR 240

Query: 241 EEWKGQAETNKILA-SPQTIPIDGLCVRVGALRCHSQAFTVKLKRDIAIPEVEQLLARHN 299
           EEWKG+AETNKIL  SP TIP++GLC+RVG +RCHS A T+KLKR++   E  +L+   +
Sbjct: 241 EEWKGEAETNKILGLSPGTIPVNGLCIRVGVIRCHSAAITLKLKREVNEEEFAELVMNSH 300

Query: 300 EWVRVIPNDRELSMRELTPAAVTGTLATPVGRLRK--LNMGPQYLSAFTVGDQLLWGAAE 357
            WV  +PN++E S+  LTPA ++G+L   +GR +K  LN  P Y S  TVGDQLLWGAAE
Sbjct: 301 PWVNYVPNNKEESVSTLTPAHISGSLKVGIGRYKKMSLNNEPIY-SVLTVGDQLLWGAAE 359

Query: 358 PLRRMLRLL 366
           PLRRML +L
Sbjct: 360 PLRRMLNIL 368


Lambda     K      H
   0.321    0.137    0.418 

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: 395
Number of extensions: 10
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS12880 BWI76_RS12880 (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.3617.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.8e-159  516.5   0.2     2e-159  516.3   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS12880  BWI76_RS12880 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS12880  BWI76_RS12880 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.3   0.2    2e-159    2e-159       1     365 [.       2     368 ..       2     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 516.3 bits;  conditional E-value: 2e-159
                               TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitc 71 
                                             k+vg+vgwrgmvgsvll+rm ee+dfd i++ ffsts +g ++p++++is++l+da+ + al e+diiitc
  lcl|FitnessBrowser__Koxy:BWI76_RS12880   2 KQVGIVGWRGMVGSVLLQRMIEENDFDNISAHFFSTSSAGAAGPVIDGISYTLKDANSVSALAEMDIIITC 72 
                                             68********************************************************************* PP

                               TIGR01745  72 qggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllms 142
                                             qggdytk iyp+l + gw gywidaas+lrm++ a iildpvn + i+ a+++gi+ fvggnc+++l lm+
  lcl|FitnessBrowser__Koxy:BWI76_RS12880  73 QGGDYTKAIYPNLLNHGWGGYWIDAASALRMDEKACIILDPVNRNNIDRAIKEGIKLFVGGNCSITLSLMG 143
                                             *********************************************************************** PP

                               TIGR01745 143 lgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelp 213
                                             l gl++ +l+ew+sv+tyq+asg+ga+++rel+ q   + +++  + +++s ++l + +kv++l+ s ++p
  lcl|FitnessBrowser__Koxy:BWI76_RS12880 144 LAGLIKADLIEWMSVMTYQSASGAGAQYVRELIAQSAYISRHLSPDELASSGSVLPLVNKVSELINSADMP 214
                                             ********************************************999999********************* PP

                               TIGR01745 214 venfsvplagslipwidkqldngqsreewkgqaetnkilgtk.dtilvdglcvrigalrchsqaltiklkk 283
                                             ++nf++pl gs+ipwid +l +g+sreewkg+aetnkilg +  ti+v+glc+r+g +rchs a+t+klk+
  lcl|FitnessBrowser__Koxy:BWI76_RS12880 215 TQNFGAPLMGSIIPWIDSDLGDGNSREEWKGEAETNKILGLSpGTIPVNGLCIRVGVIRCHSAAITLKLKR 285
                                             ****************************************87369************************** PP

                               TIGR01745 284 dvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgke.ylsaftvgdqllwg 353
                                             +v+ ee  e++ +  +wv++vpn++e ++  ltpa ++g+l++++gr +k+ + +e   s +tvgdqllwg
  lcl|FitnessBrowser__Koxy:BWI76_RS12880 286 EVNEEEFAELVMNSHPWVNYVPNNKEESVSTLTPAHISGSLKVGIGRYKKMSLNNEpIYSVLTVGDQLLWG 356
                                             ***************************************************9998834599********** PP

                               TIGR01745 354 aaeplrrmlril 365
                                             aaeplrrml+il
  lcl|FitnessBrowser__Koxy:BWI76_RS12880 357 AAEPLRRMLNIL 368
                                             **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (372 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: 11.17
//
[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