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

GapMind for Amino acid biosynthesis

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

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate CA265_RS09650 CA265_RS09650 diaminopimelate decarboxylase

Query= reanno::Btheta:350902
         (386 letters)



>FitnessBrowser__Pedo557:CA265_RS09650
          Length = 390

 Score =  417 bits (1073), Expect = e-121
 Identities = 214/386 (55%), Positives = 271/386 (70%), Gaps = 9/386 (2%)

Query: 7   IDKFRTLQTPFYYYDTKVLRDTLSAINQEVAKYPSYSVHYAVKANANPKVLTIIRESGMG 66
           I KF  ++TPFYYYDT +L+ TL       A Y  + +HYA+KAN N  +L  I+E G G
Sbjct: 7   ISKFNNIETPFYYYDTDLLQKTLRTCADAAAPY-QFHIHYALKANFNSVLLNQIKEIGFG 65

Query: 67  ADCVSGGEIRAAVRAGFPANKIVFAGVGKADWEINLGLEYGIFCFNVESIPELEVINELA 126
           ADCVS GE+R AV  GF   KIVFAGVGK+D EIN  L+  IFCFNVESI ELEV+NELA
Sbjct: 66  ADCVSAGEVRRAVEVGFDHKKIVFAGVGKSDKEINEALDLDIFCFNVESIQELEVLNELA 125

Query: 127 AAQNKIANVAFRINPDVGAHTHANITTGLAENKFGISMQDMDRVIDVALEMKNVKFIGLH 186
             + K A VA RINP+V AHTH NITTGL ENKFGI+  D+    D      N+KFIG+H
Sbjct: 126 GKKGKTAQVAIRINPNVDAHTHHNITTGLDENKFGINSWDLPECADTLKASPNLKFIGIH 185

Query: 187 FHIGSQILDMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNRQSVPDFKS 246
           FHIGSQI ++  +  LC RVNE     E +   ++ +NVGGGLGIDY +P+ Q +PDFKS
Sbjct: 186 FHIGSQITNLDVYKNLCVRVNEFAAWFEDKGFNLQVLNVGGGLGIDYHNPDHQ-IPDFKS 244

Query: 247 YFATYAGQLKLRPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGMTDLIRP 306
           YF  ++  L ++P Q +HFELGRA+VGQ  SLI++VLY+K G KK F +LDAGMT+L+RP
Sbjct: 245 YFKIFSEFLTVKPGQEVHFELGRALVGQSASLITRVLYIKNGKKKNFVVLDAGMTELMRP 304

Query: 307 ALYQAYHKMENITSEEPVEA-------YDVVGPICESSDVFGKAIDLNKVKRGDLIALRS 359
           ALYQAYHK+EN++ +  V +       YD+VGPICES+D FGK ++  +  RGD+ A+RS
Sbjct: 305 ALYQAYHKIENLSRKSEVGSPESTALKYDIVGPICESTDCFGKEVEQPESFRGDIFAIRS 364

Query: 360 AGAYGEIMASGYNCRELPKGYTSDEL 385
           AGAYGE+MAS YN R+  +   S E+
Sbjct: 365 AGAYGEVMASKYNLRDAIRSVYSSEI 390


Lambda     K      H
   0.321    0.138    0.405 

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: 425
Number of extensions: 13
Number of successful extensions: 4
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: 386
Length of database: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
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: 50 (23.9 bits)

Align candidate CA265_RS09650 CA265_RS09650 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.29606.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.9e-123  398.0   0.0   2.5e-123  397.6   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS09650  CA265_RS09650 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS09650  CA265_RS09650 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.6   0.0  2.5e-123  2.5e-123      22     393 ..      12     385 ..       5     389 .. 0.94

  Alignments for each domain:
  == domain 1  score: 397.6 bits;  conditional E-value: 2.5e-123
                                  TIGR01048  22 efgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGElerala 89 
                                                +  tP+Y yd++ l++ l++ + a + ++  ++YA+KAn n  +l+ ++e G+g+d+vs GE+ ra++
  lcl|FitnessBrowser__Pedo557:CA265_RS09650  12 NIETPFYYYDTDLLQKTLRTCADAAAPYQFHIHYALKANFNSVLLNQIKEIGFGADCVSAGEVRRAVE 79 
                                                678**********************99988************************************** PP

                                  TIGR01048  90 AgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157
                                                 g++ +kivf+g+gks++e+++al+l+i ++nv+s++ele l+e+a++ gk+a+v++R+np+vda+th
  lcl|FitnessBrowser__Pedo557:CA265_RS09650  80 VGFDHKKIVFAGVGKSDKEINEALDLDIFCFNVESIQELEVLNELAGKKGKTAQVAIRINPNVDAHTH 147
                                                ******************************************************************** PP

                                  TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkee 225
                                                  i+TGl e+KFGi+  +  e + + +++++l+ +Gih+HIGSqi++l+ +++ + +v ++++ ++++
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 148 HNITTGLDENKFGINSWDLPECADTLKASPNLKFIGIHFHIGSQITNLDVYKNLCVRVNEFAAWFEDK 215
                                                ******************************************************************** PP

                                  TIGR01048 226 gieleeldlGGGlgisyee.eeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltr 292
                                                g++l++l++GGGlgi+y++ +++ pd ++y + + e l+     +  +++ +E GR+lv++++ l+tr
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 216 GFNLQVLNVGGGLGIDYHNpDHQIPDFKSYFKIFSEFLTV----KPGQEVHFELGRALVGQSASLITR 279
                                                *****************87255678888888887766665....57999******************* PP

                                  TIGR01048 293 VesvKevesrkfvlvDagmndliRpalYeayheiaalkr.....leeeetetvdvvGplCEsgDvlak 355
                                                V ++K+ ++++fv+ Dagm++l+RpalY+ayh+i +l+r       e ++ ++d+vGp+CEs D ++k
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 280 VLYIKNGKKKNFVVLDAGMTELMRPALYQAYHKIENLSRksevgSPESTALKYDIVGPICESTDCFGK 347
                                                *************************************9955544445667899*************** PP

                                  TIGR01048 356 drelpeveeGdllavasaGAYgasmssnYnsrprpaev 393
                                                ++e pe  +Gd+ a++saGAYg  m+s+Yn r  ++ v
  lcl|FitnessBrowser__Pedo557:CA265_RS09650 348 EVEQPESFRGDIFAIRSAGAYGEVMASKYNLRDAIRSV 385
                                                *******************************9988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (390 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.66
//
[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