GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04681 H281DRAFT_04681
           glycolate oxidase iron-sulfur subunit
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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