GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Acidovorax sp. GW101-3H11

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate Ac3H11_2553 Cell division transporter, ATP-binding protein FtsE (TC 3.A.5.1.1)

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2553
          Length = 265

 Score =  225 bits (573), Expect = 8e-64
 Identities = 126/247 (51%), Positives = 162/247 (65%), Gaps = 7/247 (2%)

Query: 1   MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60
           ++ I+ + K +G   VL     +V   +V+VV GPSGSGKST ++C N LE  + G V +
Sbjct: 18  IVRIRGLRKAFGSHVVLNGIDFDVLPSQVVVVIGPSGSGKSTFLRCCNGLEQPEGGSVEI 77

Query: 61  DGTSIAD-----PKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASK 115
            G ++       P  +L  LR  VGMVFQ F LFPHLS++DN+T+   K+ G S++EA +
Sbjct: 78  CGRTLVQDGRMLPDHDLNALREEVGMVFQSFNLFPHLSVLDNVTLGPRKLRGLSRKEAEE 137

Query: 116 KALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEV 175
           +A  LL +VGL+  A   P  LSGGQ+QRVAIARALAM+P VMLFDEPTSALDPE+V EV
Sbjct: 138 RAQALLTKVGLAHKAPAMPASLSGGQKQRVAIARALAMEPRVMLFDEPTSALDPELVGEV 197

Query: 176 LDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQ 235
           L VM  LA EGMTMM VTHEM FAR+V D V+ MD G IIE       F + T   +R +
Sbjct: 198 LQVMKLLASEGMTMMVVTHEMDFAREVGDVVVVMDGGGIIEAGAPATIFTNPT--QERTR 255

Query: 236 HFLEKIL 242
            FL+ +L
Sbjct: 256 SFLQAVL 262


Lambda     K      H
   0.321    0.135    0.390 

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: 194
Number of extensions: 6
Number of successful extensions: 2
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: 244
Length of database: 265
Length adjustment: 24
Effective length of query: 220
Effective length of database: 241
Effective search space:    53020
Effective search space used:    53020
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: 47 (22.7 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