GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pseudomonas fluorescens FW300-N2E3

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AO353_04290 AO353_04290 1-pyrroline dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04290
          Length = 474

 Score =  718 bits (1853), Expect = 0.0
 Identities = 354/474 (74%), Positives = 402/474 (84%)

Query: 1   MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60
           MQ KLLING+LV+GEG  Q V+NPA G VL+EI EAS  QVDAAVRAADAAF  W QT P
Sbjct: 1   MQTKLLINGQLVTGEGPAQAVFNPALGRVLVEINEASEAQVDAAVRAADAAFEGWSQTPP 60

Query: 61  KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120
           K R+  LLKLADVI+ +G+  A+LES NCGKP  +A NDEIPAI DVFRFFAGA+RC++G
Sbjct: 61  KDRSLLLLKLADVIQAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGASRCMSG 120

Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180
            A GEYL GHTSMIRRDP+GV+ASIAPWNYPLMM AWK+APALAAGN VVLKPSE TPLT
Sbjct: 121 SAGGEYLPGHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLT 180

Query: 181 ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240
           AL+LAELA +IFPAGV+N++FGRG TVG PL  HPKVRMVSLTGSIATG +IIS TA S+
Sbjct: 181 ALRLAELASEIFPAGVLNLVFGRGPTVGSPLVTHPKVRMVSLTGSIATGSNIISSTADSV 240

Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300
           KR HMELGGKAPVI+FDDADI+A VEG+RTFG+YNAGQDCTAACRIYAQ GIY+  VEKL
Sbjct: 241 KRMHMELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIYEKFVEKL 300

Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY 360
           GAAV+++K G  DD STELGPL +  H +RV   VE A A  HI++ITGG+  +GNG+++
Sbjct: 301 GAAVSSIKYGLQDDPSTELGPLITAQHRDRVAGFVERAIAQPHIRLITGGKAVEGNGFFF 360

Query: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420
            PT+LA A QDD IV++EVFGPVVSVT F +E QV+ WANDS YGLASSVWT DVGRAHR
Sbjct: 361 EPTVLADARQDDEIVRREVFGPVVSVTSFADETQVLAWANDSDYGLASSVWTSDVGRAHR 420

Query: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           ++ARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMS+YGLEDYT VRHVM KH
Sbjct: 421 LAARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTVRHVMFKH 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: 689
Number of extensions: 20
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: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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:

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