Alignments for a candidate for asd in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Pedobacter sp. GW460-11-11-14-LB5

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate CA265_RS15395 CA265_RS15395 aspartate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-6564
         (346 letters)



>FitnessBrowser__Pedo557:CA265_RS15395
          Length = 329

 Score =  295 bits (754), Expect = 1e-84
 Identities = 160/342 (46%), Positives = 224/342 (65%), Gaps = 13/342 (3%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           + VAVVGATG VG  MLK LE+RNF +  L  ++S++S G ++TFKG++  +        
Sbjct: 1   MKVAVVGATGLVGTVMLKVLEERNFPLTELIPVASEKSVGKEITFKGKKFPIVSMDTAIS 60

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
              +IALFSAGG+ S   AP   + G  VIDN+SA+RMD    L+VPEVN  +L   N I
Sbjct: 61  MKPDIALFSAGGNTSLEHAPRFKEAGTTVIDNSSAWRMDPAIKLIVPEVNAHELSIDNKI 120

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMV  L+P+   Y + +V+VSTYQ+V+G G +AV++L ++ + +       
Sbjct: 121 IANPNCSTIQMVVVLKPLHDKYKIKRVVVSTYQSVTGTGVKAVEQLMNERKGVDG----- 175

Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244
           P+  P       Y+I  N +P ID F +NGYT EEMKM+ ET KIM    ++V AT VR+
Sbjct: 176 PKAYP-------YEIDLNVLPHIDVFMENGYTKEEMKMVKETNKIMSDDSIKVTATTVRI 228

Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304
           P+  GHSESV IE + +D  + +++++L+++PG+ + DD +   YPMP DA  K++VFVG
Sbjct: 229 PVMGGHSESVNIEFE-NDFDLAEVRSILEKSPGIIVVDDVANLKYPMPKDAHEKDEVFVG 287

Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           RIR+D       +LW+V+DNL KGAA N+VQIAE L +  LV
Sbjct: 288 RIRRDESAPKALNLWIVADNLRKGAATNAVQIAEYLIQKELV 329


Lambda     K      H
   0.314    0.131    0.366 

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: 285
Number of extensions: 8
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: 346
Length of database: 329
Length adjustment: 28
Effective length of query: 318
Effective length of database: 301
Effective search space:    95718
Effective search space used:    95718
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS15395 CA265_RS15395 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.1066.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.6e-135  436.9   3.2   4.8e-135  436.0   3.2    1.4  1  lcl|FitnessBrowser__Pedo557:CA265_RS15395  CA265_RS15395 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15395  CA265_RS15395 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.0   3.2  4.8e-135  4.8e-135       1     338 [.       2     325 ..       2     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.0 bits;  conditional E-value: 4.8e-135
                                  TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfs 68 
                                                +va+vGatG vG ++lkvLeernfp+ +l+++ase+s Gk+++fkgk++ + +++++   + dialfs
  lcl|FitnessBrowser__Pedo557:CA265_RS15395   2 KVAVVGATGLVGTVMLKVLEERNFPLTELIPVASEKSVGKEITFKGKKFPIVSMDTAISMKPDIALFS 69 
                                                69*******************************************************999******** PP

                                  TIGR01296  69 aGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvL 136
                                                aGg++s e ap++ +ag++viDn+sa+r+d+ + L+vpevna+el   +   iianPnCstiq+vvvL
  lcl|FitnessBrowser__Pedo557:CA265_RS15395  70 AGGNTSLEHAPRFKEAGTTVIDNSSAWRMDPAIKLIVPEVNAHELSIDN--KIIANPNCSTIQMVVVL 135
                                                *********************************************9988..8**************** PP

                                  TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaipli 204
                                                kpl+d++k+krvvvstYq+v G+G k+ve+L n+ k v              +k+++++i  n++p+i
  lcl|FitnessBrowser__Pedo557:CA265_RS15395 136 KPLHDKYKIKRVVVSTYQSVTGTGVKAVEQLMNERKGVD------------GPKAYPYEIDLNVLPHI 191
                                                *********************************998763............3589************* PP

                                  TIGR01296 205 dklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeap 272
                                                d ++e+Gytkee+k++ et+ki+ ++ +kv+at+vr+Pv+ ghsesv+iefe+++++ ev+ +L+++p
  lcl|FitnessBrowser__Pedo557:CA265_RS15395 192 DVFMENGYTKEEMKMVKETNKIMSDDSIKVTATTVRIPVMGGHSESVNIEFENDFDLAEVRSILEKSP 259
                                                ******************************************************************** PP

                                  TIGR01296 273 gvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                                g++v+dd  + +yp+P +a +kdevfvgrir+D s  k+l+l++vaDnlrkGaa+navqiae li+
  lcl|FitnessBrowser__Pedo557:CA265_RS15395 260 GIIVVDDVANLKYPMPKDAHEKDEVFVGRIRRDESAPKALNLWIVADNLRKGAATNAVQIAEYLIQ 325
                                                ***************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (329 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.04
# Mc/sec: 2.74
//
[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