Alignments for a candidate for patA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for patA in Klebsiella michiganensis M5al

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate BWI76_RS24630 BWI76_RS24630 putrescine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Koxy:BWI76_RS24630
          Length = 468

 Score =  865 bits (2235), Expect = 0.0
 Identities = 433/459 (94%), Positives = 447/459 (97%)

Query: 1   MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAG 60
           +NRLPSSASALACSAHALNLIEKRTLDHEEMK+LN+EV EYFKEHVNPGFL YRKSVTAG
Sbjct: 10  LNRLPSSASALACSAHALNLIEKRTLDHEEMKSLNQEVREYFKEHVNPGFLAYRKSVTAG 69

Query: 61  GDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQE 120
           GDYGAVEWQAG LNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAV+NQLAKQPLHSQE
Sbjct: 70  GDYGAVEWQAGGLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVENQLAKQPLHSQE 129

Query: 121 LLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAF 180
           LLDPLRAMLAKTLAALTPGKLKYSFF NSGTESVEAALKLAKAYQSPRGKFTF+ATSGAF
Sbjct: 130 LLDPLRAMLAKTLAALTPGKLKYSFFSNSGTESVEAALKLAKAYQSPRGKFTFVATSGAF 189

Query: 181 HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI 240
           HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFG+I AMRT L+ECKKTGDDVAAVILEPI
Sbjct: 190 HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGDINAMRTLLSECKKTGDDVAAVILEPI 249

Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300
           QGEGGVILPPPGYL AVRKLCDEFGAL+ILDEVQTGMGRTGKMFACEHENVQPDILCLAK
Sbjct: 250 QGEGGVILPPPGYLPAVRKLCDEFGALLILDEVQTGMGRTGKMFACEHENVQPDILCLAK 309

Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360
           ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLL QNLPAQAE
Sbjct: 310 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLTQNLPAQAE 369

Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN 420
           QKGDMLLDGFRQLAREYPDLV E RGKGMLMAIEFVDNEIGY+FASEMFRQRVLVAGTLN
Sbjct: 370 QKGDMLLDGFRQLAREYPDLVNEVRGKGMLMAIEFVDNEIGYDFASEMFRQRVLVAGTLN 429

Query: 421 NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA 459
           NA+TIR+EPPLTLT+EQCE V+KAAR ALAA+RVSVEEA
Sbjct: 430 NARTIRVEPPLTLTLEQCEQVLKAARLALAALRVSVEEA 468


Lambda     K      H
   0.320    0.135    0.393 

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: 24
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: 459
Length of database: 468
Length adjustment: 33
Effective length of query: 426
Effective length of database: 435
Effective search space:   185310
Effective search space used:   185310
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: 51 (24.3 bits)

Align candidate BWI76_RS24630 BWI76_RS24630 (putrescine aminotransferase)
to HMM TIGR03372 (ygjG: putrescine aminotransferase (EC 2.6.1.82))

# 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/TIGR03372.hmm
# target sequence database:        /tmp/gapView.11419.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03372  [M=442]
Accession:   TIGR03372
Description: putres_am_tran: putrescine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     3e-291  951.5   0.5   3.4e-291  951.3   0.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS24630  BWI76_RS24630 putrescine aminotr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS24630  BWI76_RS24630 putrescine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  951.3   0.5  3.4e-291  3.4e-291       1     442 []      17     458 ..      17     458 .. 1.00

  Alignments for each domain:
  == domain 1  score: 951.3 bits;  conditional E-value: 3.4e-291
                               TIGR03372   1 lsalecsaqalnliekdtldheemkalnrevleyfkeyvnpgfleyrksvtaggdygavewrasglntlvd 71 
                                             +sal+csa+alnliek+tldheemk+ln+ev eyfke+vnpgfl yrksvtaggdygavew+a+glntlvd
  lcl|FitnessBrowser__Koxy:BWI76_RS24630  17 ASALACSAHALNLIEKRTLDHEEMKSLNQEVREYFKEHVNPGFLAYRKSVTAGGDYGAVEWQAGGLNTLVD 87 
                                             589******************************************************************** PP

                               TIGR03372  72 tqgqeyldclggygifnvghrnpvvvaavesqlakqplhsqelldplrallaktlaaltpgklkysffsns 142
                                             tqgqe++dclgg+gifnvghrnpvvv+ave+qlakqplhsqelldplra+laktlaaltpgklkysffsns
  lcl|FitnessBrowser__Koxy:BWI76_RS24630  88 TQGQEFIDCLGGFGIFNVGHRNPVVVSAVENQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFSNS 158
                                             *********************************************************************** PP

                               TIGR03372 143 gtesveaalklakayqsprgkytfiaasgafhgkslgalsataksafrkpfmpllpgfrhvafgdieamlk 213
                                             gtesveaalklakayqsprgk+tf+a+sgafhgkslgalsataks+frkpfmpllpgfrhv+fgdi+am++
  lcl|FitnessBrowser__Koxy:BWI76_RS24630 159 GTESVEAALKLAKAYQSPRGKFTFVATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGDINAMRT 229
                                             *********************************************************************** PP

                               TIGR03372 214 alqeckktgddvaavilepiqgeggvilppenyltavrklcdevgallildevqtgmgrtgkmfacehenv 284
                                              l eckktgddvaavilepiqgeggvilpp++yl+avrklcde+gallildevqtgmgrtgkmfacehenv
  lcl|FitnessBrowser__Koxy:BWI76_RS24630 230 LLSECKKTGDDVAAVILEPIQGEGGVILPPPGYLPAVRKLCDEFGALLILDEVQTGMGRTGKMFACEHENV 300
                                             *********************************************************************** PP

                               TIGR03372 285 qpdilclakalgggvmpigatvateevfsvlfenpflhtttfggnplacaaalatvnvlleknlpeqaeik 355
                                             qpdilclakalgggvmpigat+ateevfsvlf+npflhtttfggnplacaaalat+nvll++nlp+qae+k
  lcl|FitnessBrowser__Koxy:BWI76_RS24630 301 QPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLTQNLPAQAEQK 371
                                             *********************************************************************** PP

                               TIGR03372 356 gellldglrqlaaeypdlvieargkgllqaiefvdneigyafakelfrrrvlvagtlnnaksvrieppltl 426
                                             g++lldg+rqla+eypdlv e rgkg+l+aiefvdneigy+fa+e+fr+rvlvagtlnna+++r+eppltl
  lcl|FitnessBrowser__Koxy:BWI76_RS24630 372 GDMLLDGFRQLAREYPDLVNEVRGKGMLMAIEFVDNEIGYDFASEMFRQRVLVAGTLNNARTIRVEPPLTL 442
                                             *********************************************************************** PP

                               TIGR03372 427 tieqcelvlkeakdvl 442
                                             t eqce+vlk+a+ +l
  lcl|FitnessBrowser__Koxy:BWI76_RS24630 443 TLEQCEQVLKAARLAL 458
                                             ************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.64
//
[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