GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcF in Paraburkholderia bryophila 376MFSha3.1

Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_04681 H281DRAFT_04681 glycolate oxidase iron-sulfur subunit

Query= reanno::Cup4G11:RR42_RS17315
         (421 letters)



>FitnessBrowser__Burk376:H281DRAFT_04681
          Length = 408

 Score =  536 bits (1380), Expect = e-157
 Identities = 261/420 (62%), Positives = 316/420 (75%), Gaps = 14/420 (3%)

Query: 1   MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLE 60
           MQT LA+F+R+TPDG+EA +I+  CVHCGFCTATCPTYQLLGDELDGPRGRIYL+KQ++E
Sbjct: 1   MQTNLADFIRNTPDGDEADAILRNCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQMVE 60

Query: 61  GQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFA 120
           G  VT+ST++HLDRCLTCRNCESTCPSGV+YG+LV+IGRK+ + +     + RP  +R  
Sbjct: 61  GAEVTRSTQVHLDRCLTCRNCESTCPSGVQYGKLVEIGRKITEKK-----VTRPLGQRLT 115

Query: 121 RWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGC 180
           R  L   +   ALF  AMR+GQ  R LLP+ LR+KVP       WP   H RKML+L GC
Sbjct: 116 RRFLASFVPNSALFTPAMRLGQHFRALLPRKLRDKVPARQRPLEWPTARHTRKMLMLAGC 175

Query: 181 VQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPA 240
           VQPSM PN+N ATARV D LGV+ ++A +AGCCGAVR H G +D  L +MR NIDAWWP 
Sbjct: 176 VQPSMMPNVNVATARVLDALGVETLVAPDAGCCGAVRLHLGYNDEALVDMRANIDAWWPY 235

Query: 241 VQAGAEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADALQDA 300
           V+ G EAIVM ASGCG  VKEY HLLR+D  YA++AR+I  LT+D++E+LP+F + L   
Sbjct: 236 VEQGVEAIVMNASGCGATVKEYAHLLRHDPAYAEKARRIVELTRDIAEILPDFEEQLASI 295

Query: 301 AAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDVKLCADSHLCCGSA 360
                    T       VA+HPPCTLQHGQQ+RG VE LLT LGV+V+L AD+HLCCGSA
Sbjct: 296 ---------TRRRAIHTVAFHPPCTLQHGQQVRGTVEHLLTRLGVEVRLPADNHLCCGSA 346

Query: 361 GTYSVLQPALSYRLRDEKLANLQALKPEAIVSANIGCITHLQSGTGTPVMHWIELVDRML 420
           GTYS+ QP LSY LRD+KL  L A +P+ IVSAN+GCI+HLQSGT TPV HWIELV+ ML
Sbjct: 347 GTYSLTQPRLSYALRDQKLERLHAQEPQMIVSANVGCISHLQSGTSTPVAHWIELVEHML 406


Lambda     K      H
   0.321    0.135    0.421 

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: 609
Number of extensions: 22
Number of successful extensions: 4
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: 421
Length of database: 408
Length adjustment: 31
Effective length of query: 390
Effective length of database: 377
Effective search space:   147030
Effective search space used:   147030
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 (21.9 bits)
S2: 50 (23.9 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