Alignments for a candidate for astB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Klebsiella michiganensis M5al

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate BWI76_RS11685 BWI76_RS11685 succinylarginine dihydrolase

Query= reanno::Koxy:BWI76_RS11685
         (441 letters)



>FitnessBrowser__Koxy:BWI76_RS11685
          Length = 441

 Score =  879 bits (2271), Expect = 0.0
 Identities = 441/441 (100%), Positives = 441/441 (100%)

Query: 1   MKAWEVNFDGLPGLTHHYAGLSFGNEASTKHRYRVSNPQLAAKQGLKKMKALADAGYPQA 60
           MKAWEVNFDGLPGLTHHYAGLSFGNEASTKHRYRVSNPQLAAKQGLKKMKALADAGYPQA
Sbjct: 1   MKAWEVNFDGLPGLTHHYAGLSFGNEASTKHRYRVSNPQLAAKQGLKKMKALADAGYPQA 60

Query: 61  LIPPQERPNIPLLRQIGFDGSDEQVLEKAARQAPELLSAASSASSMWVANAATVSPSADS 120
           LIPPQERPNIPLLRQIGFDGSDEQVLEKAARQAPELLSAASSASSMWVANAATVSPSADS
Sbjct: 61  LIPPQERPNIPLLRQIGFDGSDEQVLEKAARQAPELLSAASSASSMWVANAATVSPSADS 120

Query: 121 LDGRVHLTVANLNDKFHRASEAPTTEALLKAIFPDAQRFAVHGALPQVSLFGDEGAANHN 180
           LDGRVHLTVANLNDKFHRASEAPTTEALLKAIFPDAQRFAVHGALPQVSLFGDEGAANHN
Sbjct: 121 LDGRVHLTVANLNDKFHRASEAPTTEALLKAIFPDAQRFAVHGALPQVSLFGDEGAANHN 180

Query: 181 RLGGDYGAPGVQLFIYGRQQGGEDNPQRYPARQTLEASQAVARLNQVNPRQVIFARQNPA 240
           RLGGDYGAPGVQLFIYGRQQGGEDNPQRYPARQTLEASQAVARLNQVNPRQVIFARQNPA
Sbjct: 181 RLGGDYGAPGVQLFIYGRQQGGEDNPQRYPARQTLEASQAVARLNQVNPRQVIFARQNPA 240

Query: 241 VIDKGVFHNDVIAVSNQQVLFCHEQAFVDQPQLLQQLAQQVPGFTPLVVPASQVSVEDAV 300
           VIDKGVFHNDVIAVSNQQVLFCHEQAFVDQPQLLQQLAQQVPGFTPLVVPASQVSVEDAV
Sbjct: 241 VIDKGVFHNDVIAVSNQQVLFCHEQAFVDQPQLLQQLAQQVPGFTPLVVPASQVSVEDAV 300

Query: 301 ATYLFNSQLLSKREGGMRLILPLEAQEHPGVWRYLNRLVEGDNPIDELQVYDLRESMANG 360
           ATYLFNSQLLSKREGGMRLILPLEAQEHPGVWRYLNRLVEGDNPIDELQVYDLRESMANG
Sbjct: 301 ATYLFNSQLLSKREGGMRLILPLEAQEHPGVWRYLNRLVEGDNPIDELQVYDLRESMANG 360

Query: 361 GGPACLRLRVVLTEDERQAVNPAVMMNDALFATLNDWVGRYYRDRLTQADLADPQLLREG 420
           GGPACLRLRVVLTEDERQAVNPAVMMNDALFATLNDWVGRYYRDRLTQADLADPQLLREG
Sbjct: 361 GGPACLRLRVVLTEDERQAVNPAVMMNDALFATLNDWVGRYYRDRLTQADLADPQLLREG 420

Query: 421 REALDRLTQILRLGSVYPFQQ 441
           REALDRLTQILRLGSVYPFQQ
Sbjct: 421 REALDRLTQILRLGSVYPFQQ 441


Lambda     K      H
   0.318    0.134    0.392 

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: 863
Number of extensions: 27
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: 441
Length of database: 441
Length adjustment: 32
Effective length of query: 409
Effective length of database: 409
Effective search space:   167281
Effective search space used:   167281
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate BWI76_RS11685 BWI76_RS11685 (succinylarginine dihydrolase)
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

# 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/TIGR03241.hmm
# target sequence database:        /tmp/gapView.28759.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03241  [M=443]
Accession:   TIGR03241
Description: arg_catab_astB: succinylarginine dihydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     4e-231  753.6   0.1   4.5e-231  753.4   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS11685  BWI76_RS11685 succinylarginine d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11685  BWI76_RS11685 succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  753.4   0.1  4.5e-231  4.5e-231       1     443 []       3     440 ..       3     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 753.4 bits;  conditional E-value: 4.5e-231
                               TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaal 71 
                                             a+evnfdGl Glth+yaGlsfGn+ast+++ +vsnp+laakqGl+kmkalad+G+ q++++pqerp+i+ l
  lcl|FitnessBrowser__Koxy:BWI76_RS11685   3 AWEVNFDGLPGLTHHYAGLSFGNEASTKHRYRVSNPQLAAKQGLKKMKALADAGYPQALIPPQERPNIPLL 73 
                                             79********************************************************************* PP

                               TIGR03241  72 rklGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaet 142
                                             r++Gf Gsde+vlekaar+apellsa+ssassmw+anaatvspsad+ dgrvh+t+anln kfhr+ ea+t
  lcl|FitnessBrowser__Koxy:BWI76_RS11685  74 RQIGFDGSDEQVLEKAARQAPELLSAASSASSMWVANAATVSPSADSLDGRVHLTVANLNDKFHRASEAPT 144
                                             *********************************************************************** PP

                               TIGR03241 143 tervlkaifadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraalerepkpkryparqt 213
                                             te++lkaif d ++favh alp+v+l+GdeGaanh+rlg++y++pgv+lf+yGr++  +e +p+ryparqt
  lcl|FitnessBrowser__Koxy:BWI76_RS11685 145 TEALLKAIFPDAQRFAVHGALPQVSLFGDEGAANHNRLGGDYGAPGVQLFIYGRQQ-GGEDNPQRYPARQT 214
                                             *******************************************************9.88999********* PP

                               TIGR03241 214 leasqavarlhqleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalg 284
                                             leasqavarl+q+++++v++a+qnp+vid+Gvfhndviavsn++vlf+he+af++q q+l++l++++ ++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS11685 215 LEASQAVARLNQVNPRQVIFARQNPAVIDKGVFHNDVIAVSNQQVLFCHEQAFVDQPQLLQQLAQQVPGF- 284
                                             *****************************************************************99987. PP

                               TIGR03241 285 qelvaievpdaevsvedavssylfnsqllskedgkmllvvpeecreneavwayldelvaadgpikevkvfd 355
                                                + + vp+++vsvedav +ylfnsqllsk++g m l++p e++e++ vw+yl+ lv+ d+pi+e++v+d
  lcl|FitnessBrowser__Koxy:BWI76_RS11685 285 ---TPLVVPASQVSVEDAVATYLFNSQLLSKREGGMRLILPLEAQEHPGVWRYLNRLVEGDNPIDELQVYD 352
                                             ...8999**************************************************************** PP

                               TIGR03241 356 lresmknGGGpaclrlrvvlndaelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqllvesrta 426
                                             lresm nGGGpaclrlrvvl+++e++avnp+v+++dalfatln+wv r+yrdrl+++dladpqll+e+r+a
  lcl|FitnessBrowser__Koxy:BWI76_RS11685 353 LRESMANGGGPACLRLRVVLTEDERQAVNPAVMMNDALFATLNDWVGRYYRDRLTQADLADPQLLREGREA 423
                                             *********************************************************************** PP

                               TIGR03241 427 ldeltqilnlGsvyefq 443
                                             ld ltqil+lGsvy+fq
  lcl|FitnessBrowser__Koxy:BWI76_RS11685 424 LDRLTQILRLGSVYPFQ 440
                                             ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (441 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: 00:00:00.02
# Mc/sec: 7.55
//
[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