Alignments for a candidate for gnd in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Klebsiella michiganensis M5al

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate BWI76_RS19025 BWI76_RS19025 phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)

Query= BRENDA::Q762L5
         (468 letters)



>FitnessBrowser__Koxy:BWI76_RS19025
          Length = 468

 Score =  906 bits (2342), Expect = 0.0
 Identities = 457/468 (97%), Positives = 466/468 (99%)

Query: 1   MSKQQIGVVGMAVMGRNLALNIESRGYTVSVFNRSREKTEEVIAENPGKKLVPYYTVQEF 60
           MSKQQIGVVGMAVMGRNLALNIESRGYTVSVFNRSREKTEEVIAENPGKKLVP+YTVQEF
Sbjct: 1   MSKQQIGVVGMAVMGRNLALNIESRGYTVSVFNRSREKTEEVIAENPGKKLVPHYTVQEF 60

Query: 61  VESLETPRRILLMVKAGAGTDSAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF 120
           VESLETPRRILLMVKAGAGTDSAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF
Sbjct: 61  VESLETPRRILLMVKAGAGTDSAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF 120

Query: 121 NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILKQIAAVAEDGEPCVTYIGADGAGH 180
           NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILKQIAAVAEDGEPCVTYIGADGAGH
Sbjct: 121 NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILKQIAAVAEDGEPCVTYIGADGAGH 180

Query: 181 YVKMVHNGIEYGDMQLIAEAYALLKGGLALSNEELAQTFTEWNEGELSSYLIDITKDIFT 240
           YVKMVHNGIEYGDMQLIAEAYALLKGGLALSNEELAQTFTEWNEGELSSYLIDITKDIFT
Sbjct: 181 YVKMVHNGIEYGDMQLIAEAYALLKGGLALSNEELAQTFTEWNEGELSSYLIDITKDIFT 240

Query: 241 KKDEEGKYLVDVILDEAANKGTGKWTSQSSLDLGEPLSLITESVFARYISSLKDQRVAAS 300
           KKDEEGKYLVDVILDEAANKGTGKWTSQSSLDLGEPLSLITESVFARYISSLKDQRVAAS
Sbjct: 241 KKDEEGKYLVDVILDEAANKGTGKWTSQSSLDLGEPLSLITESVFARYISSLKDQRVAAS 300

Query: 301 KVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASDEYNWDLNYGEIAKIF 360
           KVL+GPQA+ AGDKAEF+EKVRRALYLGKIVSYAQGFSQLRAASDEY+WDLNYGEIAKIF
Sbjct: 301 KVLTGPQAKSAGDKAEFVEKVRRALYLGKIVSYAQGFSQLRAASDEYHWDLNYGEIAKIF 360

Query: 361 RAGCIIRAQFLQKITDAYAQNAGIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT 420
           RAGCIIRAQFLQKIT+AY QNAGIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT
Sbjct: 361 RAGCIIRAQFLQKITNAYEQNAGIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT 420

Query: 421 FSAAIAYYDSYRSAVLPANLIQAQRDYFGAHTYKRTDKEGIFHTEWLE 468
           FSAAIAYYDSYRSAVLPANLIQAQRDYFGAHTYKRTDKEG+FHTEW++
Sbjct: 421 FSAAIAYYDSYRSAVLPANLIQAQRDYFGAHTYKRTDKEGVFHTEWMD 468


Lambda     K      H
   0.316    0.135    0.382 

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: 860
Number of extensions: 23
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: 468
Length of database: 468
Length adjustment: 33
Effective length of query: 435
Effective length of database: 435
Effective search space:   189225
Effective search space used:   189225
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: 51 (24.3 bits)

Align candidate BWI76_RS19025 BWI76_RS19025 (phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating))
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))

# 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.carbon/TIGR00873.hmm
# target sequence database:        /tmp/gapView.29957.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00873  [M=467]
Accession:   TIGR00873
Description: gnd: 6-phosphogluconate dehydrogenase (decarboxylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     1e-232  758.9   0.3   1.2e-232  758.7   0.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS19025  BWI76_RS19025 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS19025  BWI76_RS19025 phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  758.7   0.3  1.2e-232  1.2e-232       1     467 []       5     468 .]       5     468 .] 0.99

  Alignments for each domain:
  == domain 1  score: 758.7 bits;  conditional E-value: 1.2e-232
                               TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilllv 71 
                                             +iG++G+avmG+nl+lni+++G++v+v+nr++ekt+e+++e + gkklv+ ++++efv+sle+Pr+ill+v
  lcl|FitnessBrowser__Koxy:BWI76_RS19025   5 QIGVVGMAVMGRNLALNIESRGYTVSVFNRSREKTEEVIAE-NPGKKLVPHYTVQEFVESLETPRRILLMV 74 
                                             69**************************************9.99*************************** PP

                               TIGR00873  72 kaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGs 142
                                             kaGa +d++i++l+p+l+kgdiiidGGn++++dt+rr++el+++g++f+G+GvsGGeeGa+kGPs+mpGG+
  lcl|FitnessBrowser__Koxy:BWI76_RS19025  75 KAGAGTDSAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQ 145
                                             *********************************************************************** PP

                               TIGR00873 143 keayelvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeia 212
                                             keayelv+pil++iaa +e gepc++yiG+dGaGhyvkmvhnGieygdmqliaeay llk +l ls+ee+a
  lcl|FitnessBrowser__Koxy:BWI76_RS19025 146 KEAYELVAPILKQIAAVAEdGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYALLKGGLALSNEELA 216
                                             *****************999*************************************************** PP

                               TIGR00873 213 evfeeWnegeldsylieitadilkkkdedGkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfar 283
                                             ++f+eWnegel+syli+it+di++kkde+Gk+lvd+ild+a++kGtGkWt++++ldlG P++litesvfar
  lcl|FitnessBrowser__Koxy:BWI76_RS19025 217 QTFTEWNEGELSSYLIDITKDIFTKKDEEGKYLVDVILDEAANKGTGKWTSQSSLDLGEPLSLITESVFAR 287
                                             *********************************************************************** PP

                               TIGR00873 284 vlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeia 354
                                             ++sslk++rvaask+l+gp+a++++ dk+ef+e+vr+aly++kivsyaqGf++l++as+ey wdln+geia
  lcl|FitnessBrowser__Koxy:BWI76_RS19025 288 YISSLKDQRVAASKVLTGPQAKSAG-DKAEFVEKVRRALYLGKIVSYAQGFSQLRAASDEYHWDLNYGEIA 357
                                             *********************9998.********************************************* PP

                               TIGR00873 355 liwrgGciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfy 425
                                             +i+r+Gciir++fl+ki++a+e+n  ++nllla+yfk++ +++q++lr+vva a+++gipvP++saa+++y
  lcl|FitnessBrowser__Koxy:BWI76_RS19025 358 KIFRAGCIIRAQFLQKITNAYEQNAGIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPTFSAAIAYY 428
                                             *********************************************************************** PP

                               TIGR00873 426 dgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWle 467
                                             d+yr+a+lpanl+qaqrdyfGahty+rtdk++  +fhteW++
  lcl|FitnessBrowser__Koxy:BWI76_RS19025 429 DSYRSAVLPANLIQAQRDYFGAHTYKRTDKEG--VFHTEWMD 468
                                             *******************************9..******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (468 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: 12.19
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources