Alignments for a candidate for patD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for patD in Klebsiella michiganensis M5al

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BWI76_RS13425 BWI76_RS13425 1-pyrroline dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Koxy:BWI76_RS13425
          Length = 475

 Score =  793 bits (2048), Expect = 0.0
 Identities = 384/474 (81%), Positives = 426/474 (89%)

Query: 1   MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60
           MQ+ LLING+LV+GEGE  PV+NPATG+ ++ IAEA+A QV+AAV AAD AF  W QTTP
Sbjct: 1   MQNNLLINGKLVAGEGEAVPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTTP 60

Query: 61  KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120
           + RAECLL LA+VI+E+ Q  A+LES NCGKPLH   NDE+PA+ DVFRFFAGAARCL G
Sbjct: 61  RSRAECLLALANVIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLPG 120

Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180
           +AAGEYLEGHTSMIRRDP+GVVASIAPWNYPLMMAAWKLAPALAAGNCVV+KPSEITPLT
Sbjct: 121 MAAGEYLEGHTSMIRRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLT 180

Query: 181 ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240
           ALKL ELAK+IFPAGV+N+LFGRG TVGDPLT H KVRMVSLTGSIATG HII HTASSI
Sbjct: 181 ALKLGELAKEIFPAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTASSI 240

Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300
           KRTHMELGGKAPVIVFDDADI+AVVEGVRTFG+YNAGQDCTAACRIYAQ GIYD LVEKL
Sbjct: 241 KRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIYDQLVEKL 300

Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY 360
           GAAVA+LK G P+DE+TELGPLSS AHL+RV  AV+ A+A  HI+VI GG K  GNGYYY
Sbjct: 301 GAAVASLKMGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKAPGNGYYY 360

Query: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420
            PTLLAGA Q+DAIVQ+EVFGPVVS+T F +EEQ ++WANDSQYGLASSVWT+DVGRAHR
Sbjct: 361 QPTLLAGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVGRAHR 420

Query: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           +SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMS+YGLEDYT +RHVM+KH
Sbjct: 421 LSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTIRHVMIKH 474


Lambda     K      H
   0.317    0.134    0.397 

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: 777
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: 474
Length of database: 475
Length adjustment: 33
Effective length of query: 441
Effective length of database: 442
Effective search space:   194922
Effective search space used:   194922
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_RS13425 BWI76_RS13425 (1-pyrroline dehydrogenase)
to HMM TIGR03374 (ydcW: 1-pyrroline dehydrogenase (EC 1.2.1.19))

# 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/TIGR03374.hmm
# target sequence database:        /tmp/gapView.15213.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03374  [M=472]
Accession:   TIGR03374
Description: ABALDH: 1-pyrroline dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     5e-293  957.9   1.7   5.6e-293  957.7   1.7    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS13425  BWI76_RS13425 1-pyrroline dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS13425  BWI76_RS13425 1-pyrroline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  957.7   1.7  5.6e-293  5.6e-293       1     472 []       2     473 ..       2     473 .. 1.00

  Alignments for each domain:
  == domain 1  score: 957.7 bits;  conditional E-value: 5.6e-293
                               TIGR03374   1 qdklliegklvagegekqavynpatgevileiaeasaeqvdaavraadaafaewgqttpkaraelllklad 71 
                                             q++lli+gklvagege+ +v+npatge i++iaea a+qv+aav+aad+af  w qttp++rae+ll la+
  lcl|FitnessBrowser__Koxy:BWI76_RS13425   2 QNNLLINGKLVAGEGEAVPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTTPRSRAECLLALAN 72 
                                             678******************************************************************** PP

                               TIGR03374  72 aieenaevfaklesrncgkplhavlndeipaivdvfrffagaarclsglaageyleghtsmirrdpvgvva 142
                                             +i+e a+ +akles ncgkplh+v+nde+pa++dvfrffagaarcl g+aageyleghtsmirrdpvgvva
  lcl|FitnessBrowser__Koxy:BWI76_RS13425  73 VIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLPGMAAGEYLEGHTSMIRRDPVGVVA 143
                                             *********************************************************************** PP

                               TIGR03374 143 siapwnyplmmaawklapalaagncvvlkpseitpltalklaelakdilpagvvnvlfgrgktvgdaltgh 213
                                             siapwnyplmmaawklapalaagncvv+kpseitpltalkl elak+i+pagv+nvlfgrg+tvgd+lt h
  lcl|FitnessBrowser__Koxy:BWI76_RS13425 144 SIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLTALKLGELAKEIFPAGVLNVLFGRGATVGDPLTAH 214
                                             *********************************************************************** PP

                               TIGR03374 214 ekvrmvsltgsiatgehilahtaasikrthmelggkapvivfddadidavvegvrtfgfynagqdctaacr 284
                                              kvrmvsltgsiatg+hi+ hta+sikrthmelggkapvivfddadidavvegvrtfgfynagqdctaacr
  lcl|FitnessBrowser__Koxy:BWI76_RS13425 215 AKVRMVSLTGSIATGAHIIGHTASSIKRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACR 285
                                             *********************************************************************** PP

                               TIGR03374 285 iyaqrgiydelveklgkavatlkigapedestelgplsslahlervsaaveeakalshikvitggekvkgk 355
                                             iyaq giyd+lveklg+ava+lk+g pede+telgplss+ahl+rvsaav+ a+al+hi+vi+gg+k+ g+
  lcl|FitnessBrowser__Koxy:BWI76_RS13425 286 IYAQAGIYDQLVEKLGAAVASLKMGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKAPGN 356
                                             *********************************************************************** PP

                               TIGR03374 356 gyyfaptllagakqddaivqkevfgpvvsitvfddeeqvvrwandsryglassvwtkdvgrahrlsarlqy 426
                                             gyy++ptllaga+q+daivq+evfgpvvsit+f deeq ++wands+yglassvwt+dvgrahrlsarlqy
  lcl|FitnessBrowser__Koxy:BWI76_RS13425 357 GYYYQPTLLAGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVGRAHRLSARLQY 427
                                             *********************************************************************** PP

                               TIGR03374 427 gctwvnthfmlvsemphggqklsgygkdmslygledytvvrhimvk 472
                                             gctwvnthfmlvsemphggqklsgygkdms+ygledyt +rh+m+k
  lcl|FitnessBrowser__Koxy:BWI76_RS13425 428 GCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTIRHVMIK 473
                                             ********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (472 nodes)
Target sequences:                          1  (475 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.16
//
[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