GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Klebsiella michiganensis M5al

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate BWI76_RS02330 BWI76_RS02330 aspartate ammonia-lyase

Query= BRENDA::P0AC38
         (478 letters)



>FitnessBrowser__Koxy:BWI76_RS02330
          Length = 478

 Score =  875 bits (2260), Expect = 0.0
 Identities = 437/478 (91%), Positives = 457/478 (95%)

Query: 1   MSNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAM 60
           M NNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAA 
Sbjct: 1   MLNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAQ 60

Query: 61  ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLE 120
           ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDV+QGGAGTSVNMNTNEVLANIGLE
Sbjct: 61  ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVFQGGAGTSVNMNTNEVLANIGLE 120

Query: 121 LMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVE 180
           LMGHQKGEYQ+LNPNDHVNKCQSTNDAYPTGFRIAVY+S++KL+DAINQL EGF++KAVE
Sbjct: 121 LMGHQKGEYQHLNPNDHVNKCQSTNDAYPTGFRIAVYASILKLIDAINQLSEGFQQKAVE 180

Query: 181 FQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLN 240
           FQDILKMGRTQLQDAVPMTLGQEF AF++LL EE K I RTAELLLEVNLGATAIGT LN
Sbjct: 181 FQDILKMGRTQLQDAVPMTLGQEFHAFNVLLNEETKCILRTAELLLEVNLGATAIGTRLN 240

Query: 241 TPKEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRL 300
           TP  Y  LAV+KLAEV+  P VPAEDLIEATSDCGAYVMVH +LKRLAVK+SKICNDLRL
Sbjct: 241 TPDGYQQLAVQKLAEVSNLPVVPAEDLIEATSDCGAYVMVHSSLKRLAVKLSKICNDLRL 300

Query: 301 LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQ 360
           LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMA+EAGQLQ
Sbjct: 301 LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMASEAGQLQ 360

Query: 361 LNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIG 420
           LNVMEPVIGQAMFES+HILTNACYNLLEKC++GITANK VCE YVYNSIGIVTYLNP+IG
Sbjct: 361 LNVMEPVIGQAMFESIHILTNACYNLLEKCVSGITANKAVCESYVYNSIGIVTYLNPYIG 420

Query: 421 HHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ 478
           HHNGDIVGKICAETGKSVR+VVLERGLLT AELDDIFS QNLMHPAYKAKRYTDESEQ
Sbjct: 421 HHNGDIVGKICAETGKSVRDVVLERGLLTAAELDDIFSAQNLMHPAYKAKRYTDESEQ 478


Lambda     K      H
   0.317    0.134    0.381 

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: 782
Number of extensions: 12
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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_RS02330 BWI76_RS02330 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

# 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/TIGR00839.hmm
# target sequence database:        /tmp/gapView.20161.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00839  [M=468]
Accession:   TIGR00839
Description: aspA: aspartate ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.4e-267  873.2   6.3   2.8e-267  873.0   6.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS02330  BWI76_RS02330 aspartate ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS02330  BWI76_RS02330 aspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  873.0   6.3  2.8e-267  2.8e-267       1     468 []       6     474 ..       6     474 .. 1.00

  Alignments for each domain:
  == domain 1  score: 873.0 bits;  conditional E-value: 2.8e-267
                               TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakai 71 
                                             rie+dllG++ev+a++yyG++tlra+enf+isn+kisd+pefv+++v+vkkaaa an+el++i++++a+ai
  lcl|FitnessBrowser__Koxy:BWI76_RS02330   6 RIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAQANKELQTIPKSVANAI 76 
                                             89********************************************************************* PP

                               TIGR00839  72 vaacdeile.GkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstnda 141
                                             +aacde+l+ Gk++dqf+vdv+qGGaGtsvnmntnev+an++lel+Gh+kGeyq+lnpndhvnk+qstnda
  lcl|FitnessBrowser__Koxy:BWI76_RS02330  77 IAACDEVLNnGKCMDQFPVDVFQGGAGTSVNMNTNEVLANIGLELMGHQKGEYQHLNPNDHVNKCQSTNDA 147
                                             ********99************************************************************* PP

                               TIGR00839 142 yptalkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkri 212
                                             ypt+++iavy s+ kl+d+i++l ++f+qka+ef+d+lkmGrtqlqdavp+tlGqef+a+ +ll+++ k i
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 148 YPTGFRIAVYASILKLIDAINQLSEGFQQKAVEFQDILKMGRTQLQDAVPMTLGQEFHAFNVLLNEETKCI 218
                                             *********************************************************************** PP

                               TIGR00839 213 krtrelllevnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriav 283
                                              rt+elllevnlGataiGt ln++++y++l+v+klaev+ lp+vpae+lieatsd+gayv+v+++lkr+av
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 219 LRTAELLLEVNLGATAIGTRLNTPDGYQQLAVQKLAEVSNLPVVPAEDLIEATSDCGAYVMVHSSLKRLAV 289
                                             *********************************************************************** PP

                               TIGR00839 284 klskvcndlrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlq 354
                                             klsk+cndlrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvt+a+eaGqlq
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 290 KLSKICNDLRLLSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMASEAGQLQ 360
                                             *********************************************************************** PP

                               TIGR00839 355 lnvlepviafallesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakea 425
                                             lnv+epvi++a++esi+iltna+++l++kcv Gitan+ +ce+yv+nsiGivt+lnp+iG++++++v+k++
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 361 LNVMEPVIGQAMFESIHILTNACYNLLEKCVSGITANKAVCESYVYNSIGIVTYLNPYIGHHNGDIVGKIC 431
                                             *********************************************************************** PP

                               TIGR00839 426 iktgksvrdvvlekdllteeelddilsvenllkpaykakklkd 468
                                             ++tgksvrdvvle++llt +elddi+s++nl++paykak+++d
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 432 AETGKSVRDVVLERGLLTAAELDDIFSAQNLMHPAYKAKRYTD 474
                                             ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (478 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.40
//
[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:

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