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

GapMind for catabolism of small carbon sources

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

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate CA265_RS14455 CA265_RS14455 L-lysine 6-transaminase

Query= reanno::Pedo557:CA265_RS14455
         (443 letters)



>FitnessBrowser__Pedo557:CA265_RS14455
          Length = 443

 Score =  905 bits (2338), Expect = 0.0
 Identities = 443/443 (100%), Positives = 443/443 (100%)

Query: 1   MYQLTVPADRVNESLSKHILADGFDLTYDMEKSHGAYIYDAKHNRTLLDFFTCFASVPLG 60
           MYQLTVPADRVNESLSKHILADGFDLTYDMEKSHGAYIYDAKHNRTLLDFFTCFASVPLG
Sbjct: 1   MYQLTVPADRVNESLSKHILADGFDLTYDMEKSHGAYIYDAKHNRTLLDFFTCFASVPLG 60

Query: 61  YNHPKMINDEAFKKNLFLAALANPSNSDVYTQQYAQFVETFSKVGIPDYLPHAFFIAGGG 120
           YNHPKMINDEAFKKNLFLAALANPSNSDVYTQQYAQFVETFSKVGIPDYLPHAFFIAGGG
Sbjct: 61  YNHPKMINDEAFKKNLFLAALANPSNSDVYTQQYAQFVETFSKVGIPDYLPHAFFIAGGG 120

Query: 121 LAVENAIKVAMDWKVQKNFAKGYTEEKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFA 180
           LAVENAIKVAMDWKVQKNFAKGYTEEKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFA
Sbjct: 121 LAVENAIKVAMDWKVQKNFAKGYTEEKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFA 180

Query: 181 KFDWPRVAVPEVKFPLSGNNLSHAIQTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGD 240
           KFDWPRVAVPEVKFPLSGNNLSHAIQTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGD
Sbjct: 181 KFDWPRVAVPEVKFPLSGNNLSHAIQTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGD 240

Query: 241 NHLREEFLIQIKALADENDAFLIYDEVQTGVGLTGKFWCHQHFSEKARPDILAFGKKMQV 300
           NHLREEFLIQIKALADENDAFLIYDEVQTGVGLTGKFWCHQHFSEKARPDILAFGKKMQV
Sbjct: 241 NHLREEFLIQIKALADENDAFLIYDEVQTGVGLTGKFWCHQHFSEKARPDILAFGKKMQV 300

Query: 301 CGILVGHKVDQVETNVFKVPSRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYL 360
           CGILVGHKVDQVETNVFKVPSRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYL
Sbjct: 301 CGILVGHKVDQVETNVFKVPSRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYL 360

Query: 361 KDQLENLSHRFDQMTNVRGRGLLCSFDFPTKEMRNTFIAKGLENNVMFLGCGEKTIRFRP 420
           KDQLENLSHRFDQMTNVRGRGLLCSFDFPTKEMRNTFIAKGLENNVMFLGCGEKTIRFRP
Sbjct: 361 KDQLENLSHRFDQMTNVRGRGLLCSFDFPTKEMRNTFIAKGLENNVMFLGCGEKTIRFRP 420

Query: 421 ALCIEQKHIDEGLTVMDKILPLL 443
           ALCIEQKHIDEGLTVMDKILPLL
Sbjct: 421 ALCIEQKHIDEGLTVMDKILPLL 443


Lambda     K      H
   0.321    0.137    0.414 

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: 848
Number of extensions: 17
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: 443
Length of database: 443
Length adjustment: 32
Effective length of query: 411
Effective length of database: 411
Effective search space:   168921
Effective search space used:   168921
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate CA265_RS14455 CA265_RS14455 (L-lysine 6-transaminase)
to HMM TIGR03251 (lat: L-lysine 6-transaminase (EC 2.6.1.36))

# 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/TIGR03251.hmm
# target sequence database:        /tmp/gapView.19524.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03251  [M=433]
Accession:   TIGR03251
Description: LAT_fam: L-lysine 6-transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-193  629.6   0.0   1.2e-193  629.4   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS14455  CA265_RS14455 L-lysine 6-transam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS14455  CA265_RS14455 L-lysine 6-transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.4   0.0  1.2e-193  1.2e-193       1     432 [.       8     440 ..       8     441 .. 0.99

  Alignments for each domain:
  == domain 1  score: 629.4 bits;  conditional E-value: 1.2e-193
                                  TIGR03251   1 adrvkevlsrhlladGldlvldleksrGsvlvdardGrryldlfsffassalGmnhPaladdaefrer 68 
                                                adrv+e ls+h+ladG+dl  d+eks+G++++da++ r++ld+f+ fas +lG+nhP++ +d++f+++
  lcl|FitnessBrowser__Pedo557:CA265_RS14455   8 ADRVNESLSKHILADGFDLTYDMEKSHGAYIYDAKHNRTLLDFFTCFASVPLGYNHPKMINDEAFKKN 75 
                                                589***************************************************************** PP

                                  TIGR03251  69 laavavnkpsnsdvytvemarfvdtfarvlvdpalPhlffieGGalavenalktafdwksrkneargi 136
                                                l  +a+  psnsdvyt+++a+fv+tf++v ++++lPh+ffi GG lavena+k+a+dwk++kn a+g+
  lcl|FitnessBrowser__Pedo557:CA265_RS14455  76 LFLAALANPSNSDVYTQQYAQFVETFSKVGIPDYLPHAFFIAGGGLAVENAIKVAMDWKVQKNFAKGY 143
                                                ******************************************************************** PP

                                  TIGR03251 137 eaelGtkvlhlrqafhGrsGytlsltntdPrktarfPkfdwPridaPkltfpldaeeldavkaleeea 204
                                                ++e+G kvlh+++afhGr+Gytlsltnt P kt++f kfdwPr+  P+++fpl++++l + +++ee++
  lcl|FitnessBrowser__Pedo557:CA265_RS14455 144 TEEKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFAKFDWPRVAVPEVKFPLSGNNLSHAIQTEETS 211
                                                ******************************************************************** PP

                                  TIGR03251 205 laqakaafaeeeddiaaliiePiqgeGGdnhlrpeflralrklcdehdallvldevqtGvGltGkawa 272
                                                laq+k+a+a+++ddi a+i+ePiq+eGGdnhlr efl ++++l+de+da+l++devqtGvGltGk+w 
  lcl|FitnessBrowser__Pedo557:CA265_RS14455 212 LAQIKKAIADNKDDICAIIVEPIQSEGGDNHLREEFLIQIKALADENDAFLIYDEVQTGVGLTGKFWC 279
                                                ******************************************************************** PP

                                  TIGR03251 273 yqqlg..vkPdvvafGkktqvcGilagrrvdevadnvfkvssrlnstfGGnlvdmvratrileiieee 338
                                                +q++    +Pd++afGkk qvcGil g++vd+v++nvfkv+sr+nst+GGnlvdmvr t+il+i+ee+
  lcl|FitnessBrowser__Pedo557:CA265_RS14455 280 HQHFSekARPDILAFGKKMQVCGILVGHKVDQVETNVFKVPSRINSTWGGNLVDMVRSTQILQIVEED 347
                                                ****63378*********************************************************** PP

                                  TIGR03251 339 rlvdrareqGehllarleelaaefpklvsnprGrGllcafdlpstelrdelvkalyrekvlvlgaGek 406
                                                +l ++a+++G +l+ +le+l+++f   ++n+rGrGllc+fd p++e+r+ ++ +  +++v+ lg+Gek
  lcl|FitnessBrowser__Pedo557:CA265_RS14455 348 QLCENATKVGLYLKDQLENLSHRFD-QMTNVRGRGLLCSFDFPTKEMRNTFIAKGLENNVMFLGCGEK 414
                                                ************************9.789*************************************** PP

                                  TIGR03251 407 airfrpaltvseeeidealdairrvl 432
                                                +irfrpal + +++ide+l +++++l
  lcl|FitnessBrowser__Pedo557:CA265_RS14455 415 TIRFRPALCIEQKHIDEGLTVMDKIL 440
                                                *********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (433 nodes)
Target sequences:                          1  (443 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: 11.16
//
[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