GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS13425 BWI76_RS13425 1-pyrroline
           dehydrogenase
          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)

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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