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.15283.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.96
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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