Alignments for a candidate for aroG in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Klebsiella michiganensis M5al

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate BWI76_RS21480 BWI76_RS21480 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__Koxy:BWI76_RS21480
          Length = 356

 Score =  655 bits (1691), Expect = 0.0
 Identities = 325/356 (91%), Positives = 341/356 (95%)

Query: 1   MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60
           MQKDALNNVHITDEQVL+TP+QLKA FPLS++QEAQIA SR++ISDIIAGRDPRLLVVCG
Sbjct: 1   MQKDALNNVHITDEQVLITPDQLKAEFPLSVEQEAQIAHSRQTISDIIAGRDPRLLVVCG 60

Query: 61  PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120
           PCSIHDPETA+EYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV
Sbjct: 61  PCSIHDPETAIEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120

Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180
           E GL+IAR LL+ELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL
Sbjct: 121 EGGLKIARHLLVELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180

Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKAP 240
           SMPVGFKNGTDGSLATAINAMRAAA PHRFVGINQAGQV LLQTQGNP+GHVILRGGKAP
Sbjct: 181 SMPVGFKNGTDGSLATAINAMRAAAMPHRFVGINQAGQVCLLQTQGNPNGHVILRGGKAP 240

Query: 241 NYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGL 300
           NY P DVA+CEKEM QAGL+PSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGL
Sbjct: 241 NYGPEDVAKCEKEMTQAGLKPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGL 300

Query: 301 MIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTARVA 356
           MIESNIHEGNQSSEQPR +MKYGVSVTDACISWE TDALLRE+ +DL G L AR+A
Sbjct: 301 MIESNIHEGNQSSEQPRCDMKYGVSVTDACISWETTDALLRELDKDLRGHLAARLA 356


Lambda     K      H
   0.316    0.131    0.378 

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: 593
Number of extensions: 10
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: 356
Length of database: 356
Length adjustment: 29
Effective length of query: 327
Effective length of database: 327
Effective search space:   106929
Effective search space used:   106929
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: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS21480 BWI76_RS21480 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.22727.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase
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-176  569.6   0.0     1e-175  569.4   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS21480  BWI76_RS21480 phospho-2-dehydro-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS21480  BWI76_RS21480 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  569.4   0.0    1e-175    1e-175       5     340 ..       8     349 ..       4     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 569.4 bits;  conditional E-value: 1e-175
                               TIGR00034   5 ivki...delltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlk 72 
                                             +v+i   + l+tP++lka+fpl+ ++++++a+sr++i+di+aG+d+rllvv+GPcsihdpe+a+eya+r+k
  lcl|FitnessBrowser__Koxy:BWI76_RS21480   8 NVHItdeQVLITPDQLKAEFPLSVEQEAQIAHSRQTISDIIAGRDPRLLVVCGPCSIHDPETAIEYARRFK 78 
                                             44444315577************************************************************ PP

                               TIGR00034  73 klaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldti 143
                                             +la++++d+l++vmrvyfekPrttvGWkGlindP++++sfdv+ Gl+iar+ll++lv++glplate+ld++
  lcl|FitnessBrowser__Koxy:BWI76_RS21480  79 ALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEGGLKIARHLLVELVNMGLPLATEALDPN 149
                                             *********************************************************************** PP

                               TIGR00034 144 spqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqva 214
                                             spqyl+dl+sw+aiGarttesq+hre+asgls+pvgfkngtdGsl++ai+a+raaa +h+f+++++aGqv+
  lcl|FitnessBrowser__Koxy:BWI76_RS21480 150 SPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSLATAINAMRAAAMPHRFVGINQAGQVC 220
                                             *********************************************************************** PP

                               TIGR00034 215 ivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqia 285
                                             +++t+Gn++gh+ilrGGk+pny +edva++++e+++aglk++lm+d+shgnsnkdy+rq++vaesvv+qi+
  lcl|FitnessBrowser__Koxy:BWI76_RS21480 221 LLQTQGNPNGHVILRGGKAPNYGPEDVAKCEKEMTQAGLKPSLMVDCSHGNSNKDYRRQPAVAESVVAQIK 291
                                             *********************************************************************** PP

                               TIGR00034 286 eGekaiiGvmiesnleeGnqslke...elkyGksvtdacigwedteallrklaeavke 340
                                             +G+++iiG+miesn++eGnqs+++   ++kyG+svtdaci+we+t+allr+l ++++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS21480 292 DGNRSIIGLMIESNIHEGNQSSEQprcDMKYGVSVTDACISWETTDALLRELDKDLRG 349
                                             *********************96522269************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (356 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: 10.32
//
[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