GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Herbaspirillum seropedicae SmR1

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate HSERO_RS01260 HSERO_RS01260 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>FitnessBrowser__HerbieS:HSERO_RS01260
          Length = 795

 Score = 1088 bits (2815), Expect = 0.0
 Identities = 549/808 (67%), Positives = 648/808 (80%), Gaps = 14/808 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           +SNFIVKKVAVLGAGVMGAQIAAH INARVPVVLFDLPAKEGPKNGI  RAIENLKKLSP
Sbjct: 1   VSNFIVKKVAVLGAGVMGAQIAAHCINARVPVVLFDLPAKEGPKNGIVQRAIENLKKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           APLG K++A LIQ ANYEDD+A+L+ CDL+IEAIAERMDWKHDLYKKVAPH+   AIFA+
Sbjct: 61  APLGNKDDAALIQVANYEDDLAVLEGCDLIIEAIAERMDWKHDLYKKVAPHIGPKAIFAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSI ALS+GFDA LK+RFCGVHFFNPPRYMHLVELIPT +T+P ILDQLEAFLTTT
Sbjct: 121 NTSGLSINALSEGFDAGLKARFCGVHFFNPPRYMHLVELIPTQSTEPHILDQLEAFLTTT 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRA DTPNF+ANRVG+F ILA   EAEK+G+  DVVDDLTG+KLGRAKS TFRTA
Sbjct: 181 LGKGVVRAFDTPNFVANRVGVFGILATIIEAEKYGLSVDVVDDLTGAKLGRAKSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTM HVI+TMQD L DDPF   Y TP +L  LV+ GALGQK+GAGFYKK GK I 
Sbjct: 241 DVVGLDTMGHVIRTMQDNLKDDPFFSSYATPPLLAKLVEQGALGQKSGAGFYKKVGKDIL 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359
            +D   G YV  G KAD+I+ R+LK KD  +R+K L +STNPQ QFLWA+FRD FHYIAV
Sbjct: 301 RIDPAKGDYVPGGAKADDIIARILKEKDPVKRMKALHDSTNPQGQFLWAIFRDAFHYIAV 360

Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAW 419
           +LE +A +A D+D A+RWGFGW+ GPFE WQ+AGWKQ+A+WVKED++AGKALS APLP W
Sbjct: 361 HLESVADNARDLDFAMRWGFGWSVGPFETWQAAGWKQIAQWVKEDIDAGKALSTAPLPDW 420

Query: 420 VFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVE 479
           VF+G      GVH+  GS+SP+ ++ VARS+LPVYQRQAFRA + G  AAD + AG T  
Sbjct: 421 VFDG----RDGVHSEKGSYSPSKKADVARSELPVYQRQAFRAPLVGEGAADGKSAGTTFF 476

Query: 480 ENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQL 539
           E+++VRIW     DDVL++SFK+KM+ IG  VIDG+ +A+  AE  +KGLV+W P +   
Sbjct: 477 EDESVRIW--HQNDDVLILSFKTKMHVIGQGVIDGMNKAVSEAEQNFKGLVIWHPDA--- 531

Query: 540 GAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGG 599
            A GG FSAGA+L++ +P FM GG K IEP V + Q    R+KYASVPV++A +G+ALGG
Sbjct: 532 -AEGGAFSAGADLQSMLPLFMSGGVKAIEPVVHQLQQAHQRLKYASVPVIAAVAGLALGG 590

Query: 600 GCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTS 659
           GCEL+LH+A RV ++E+YIGLVEVGVGL+PAGGGLKEAA+ AAR A+     +IL FL  
Sbjct: 591 GCELLLHTAKRVVSIESYIGLVEVGVGLIPAGGGLKEAAVRAAREAK---GNDILPFLKE 647

Query: 660 RFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTLV 719
              +AA A VS SALEAR++GYL+  D IVFN +ELL+VA+ E RAL  AGYR  LP  V
Sbjct: 648 YMLAAATANVSKSALEARKLGYLREDDVIVFNPYELLHVAKVEARALFDAGYRPQLPPQV 707

Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779
           PV GR+G+ATI A LVNMRDGGFIS HDF +   IAE V GG+VE GS+V+E WLL +ER
Sbjct: 708 PVIGRNGLATIMAQLVNMRDGGFISAHDFKLGKMIAETVSGGEVEEGSIVNEQWLLDIER 767

Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           K F++LL   KTQERIMGM+QTGKPVRN
Sbjct: 768 KFFMELLNHPKTQERIMGMMQTGKPVRN 795


Lambda     K      H
   0.319    0.134    0.391 

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: 1714
Number of extensions: 71
Number of successful extensions: 6
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: 807
Length of database: 795
Length adjustment: 41
Effective length of query: 766
Effective length of database: 754
Effective search space:   577564
Effective search space used:   577564
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: 55 (25.8 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